No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Taxonomic Note: a Place for DNA-DNA Reassociation and 16s rRNA Sequence Analysis in the Present Species Definition in Bacteriology
Abstract
Because a natural entity 'species' cannot be recognized as a group of strains that is genetically well separated from its phylogenetic neighbors, a pragmatic approach was taken to define a species by a polyphasic approach (L. G. Wayne, D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Truper, Int. J. Syst. Bacteriol. 37:463-464, 1987), in which a DNA reassociation value of about 70% plays a dominant role. With the establishment of rapid sequence analysis of 16S rRNA and the recognition of its potential to determine the phylogenetic position of any prokaryotic organism, the role of 16S rRNA similarities in the present species definition in bacteriology needs to be clarified. Comparative studies clearly reveal the limitations of the sequence analysis of this conserved gene and gene product in the determination of relationships at the strain level for which DNA-DNA reassociation experiments still constitute the superior method. Since today the primary structure of 16S rRNA is easier to determine than hybridization between DNA strands, the strength of the sequence analysis is to recognize the level at which DNA pairing studies need to be performed, which certainly applies to similarities of 97% and higher.
... The comparison of 16S rRNA gene sequences is a reliable way to evaluate the affiliation of bacterial species. The similarity of 16S rRNA gene sequences higher than 97% between bacterial strains could be considered as a generally accepted criterion to delineate them as the same species (Stackebrandt and Goebel, 1994). After sequencing the amplified fragments obtained from the universal primers of 27 F and 1492 R, 1528 bp complete sequence of 16S rRNA gene from strain L3 was deposited at Genbank with the accession number of ON909190. ...
... Raw FASTQ files were de-multiplexed using an in-house perl script, and then quality-filtered by fastp version 0.19.6 (Chen et al., 2018) and merged by FLASH version 1.2.7 (Magoč & Salzberg, 2011). Then the optimized sequences were clustered into OTUs using UPARSE 7.1 (Edgar, 2013;Stackebrandt and Goebel, 1994) with 97% sequence similarity level. The most abundant sequence for each OTU was selected as a representative sequence. ...
The deterioration of the quality of raw liquor caused by the low content of ethyl hexanoate in Nongxiangxing baijiu has become a pervasive problem in the baijiu industry. Therefore, this study attempted to increase the synthesis of ethyl hexanoate by microorganisms with high esterase activity to increase Zaopei fermentation. The results showed that biofortification was a feasible and important way to improve the quality of the raw liquor and increase the ethyl hexanoate content. Adding Bacillus subtilis, Staphylococcus epidermidis, and Millerozyma farinosa for biofortified fermentation disturbed the microbial community structure of Zaopei and increased the abundance of Wickerhamomyces, Saccharomyces, and Thermoascus. The contents of ethyl hexanoate, ethyl valerate, ethyl caprylate, and ethyl heptanoate also increased noticeably in baijiu. The results of E‐nose and sensory analysis tested and verified that the baijiu in the fortified group had better flavor characteristics.
... 3.2 Determination of MGB via 16S rDNA and housekeeping gene sequencing 3.2.1 Determination of MGB via 16S rRNA sequencing rRNA sequencing has commonly been utilized for the identification of bacterial species. Bacterial taxonomists have proposed criteria of 97 and 98.65% similarity in the 16S rDNA sequence to distinguish between two bacterial species (Stackebrandt and Goebel, 1994;Kim et al., 2014). Nevertheless, the effectiveness of 16S rDNA analysis is intrinsically constrained due to the high prevalence of conserved regions within the 16S rDNA sequence (Ferraz Helene et al., 2022). ...
Everything about Mangrovibacter 😁
... We tested two 16S rRNA gene similarity thresholds within the Laspinema genus, 97.5% (Stackebrandt & Goebel, 1994) and 98.7% (Stackebrandt & Ebers, 2006). We did not identify any specific species clustering, but rather several divergent strains, which revealed similarities below the threshold. ...
Cyanobacterial taxonomy is entering the genomic era, but only a few taxo-
nomic studies have employed population genomics, which provides a frame-
work and a multitude of tools to understand species boundaries. Phylogenomic
and population genomic analyses previously suggested that several cryptic
lineages emerged within the genus Laspinema. Here, we apply population
genomics to define boundaries between these lineages and propose two new
cryptic species, Laspinema olomoucense and L. palackyanum. Moreover,
we sampled soil and puddles across Central Europe and sequenced the
16S rRNA gene and 16S-23S ITS region of the isolated Laspinema strains.
Together with database mining of 16S rRNA gene sequences, we determined
that the genus Laspinema has a cosmopolitan distribution and inhabits a
wide variety of habitats, including freshwater,
... The ANI (average nucleotide identity) values between strain MAH-18 T (Table S2). These ANI values and dDDH values are well below than the species threshold of 95-96 and 70 %, respectively, suggesting that MAH-18 T represents a novel species [27][28][29]. The phylogenetic tree that was reconstructed from multi-locus sequence analysis of whole-genome sequences showed that strain MAH-18 T is clustered with the members of genus Nocardioides (Fig. S2). ...
A novel bacterial strain, designated as MAH-18 T , was isolated from soil sampled in a flower garden. Cells of strain MAH-18 T were Gram-stain-positive, aerobic, motile, and rod-shaped. The colonies were beige in colour, smooth, and spherical when grown on Reasoner's 2A agar medium. Strain MAH-18 T grew at 20–40 °C, pH 6.0–8.0, and 0–1.0 % NaCl. Cells were able to hydrolyse aesculin, gelatin, and Tween 20. According to the 16S rRNA gene sequence comparisons, the isolate was determined to be a member of the genus Nocardioides and most closely related to Nocardioides pyridinolyticus OS4 T (97.9 %), Nocardioides hankookensis DS-30 T (97.9 %), Nocardioides aquiterrae GW-9 T (97.6 %), Nocardioides soli mbc-2 T (97.5 %), Nocardioides conyzicola HWE 2-02 T (97.4 %), and Nocardioides mangrovi GBK3QG-3 T (96.3 %). Strain MAH-18 T has a draft genome size of 4 788 325 bp (eight contigs), 4572 protein-coding genes, 46 tRNA, and three rRNA genes. The average nucleotide identity and digital DNA–DNA hybridization values between strain MAH-18 T and the closest type strains were 81.5–83.4 % and 24.4–25.8 %, respectively. In silico genome mining revealed several biosynthetic gene clusters in the genome of the novel strain MAH-18 T . The G+C content of the genomic DNA of strain was 72.2 mol% and the predominant isoprenoid quinone was MK-8 (H 4 ). The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and unknown phospholipids. The major cellular fatty acids were determined to be C 16:0 iso and C 17 : 1 ω 6 c . The DNA–DNA hybridization results and phenotypic, genotypic, and chemotaxonomic data demonstrated that strain MAH-18 T represents a novel species, for which the name Nocardioides agri sp. nov. is proposed, with MAH-18 T as the type strain (=KACC 19744 T =CGMCC 1.13656 T ).
... (15) with the usage criteria. Operational taxonomic unit (OTU) clustering and chimera removal were performed on the quality-controlled spliced sequences based on 97% similarity using UPARSE v11 software (16,17). To minimize the impact of the sequencing depth on the subsequent analysis of alpha and beta diversity data, the number of sequences in all samples was rarefied to 20,000. ...
Background
Type 1 Diabetes Mellitus (T1DM) is one of the most common endocrine disorders of childhood and adolescence, showing a rapidly increasing prevalence worldwide. A study indicated that the composition of the oropharyngeal and gut microbiota changed in T1DM. However, no studies have yet associated the changes between the microbiomes of the oropharyngeal and intestinal sites, nor between the flora and clinical indicators. In this study, we examined the composition and characteristics of oropharyngeal and intestinal flora in patients with T1DM in compared to healthy children. We identified correlations between oropharyngeal and intestinal flora and evaluated their association with clinical laboratory tests in patients with T1DM.
Methods
The oropharyngeal and fecal samples from 13 T1DM and 20 healthy children were analyzed by high-throughput sequencing of the V3–V4 region of 16S rRNA. The associations between microbes and microorganisms in oropharyngeal and fecal ecological niches, as well as the correlation between these and clinical indicators were further analyzed.
Results
It was revealed that T1DM children had distinct microbiological characteristics, and the dominant oropharyngeal microbiota genus included Streptococcus, Prevotella, Leptotrichia, and Neisseria; that of intestinal microbiota included Blautia, Fusicatenibacter, Bacteroides, and Eubacterium_hallii_group. Furthermore, oropharyngeal Staphylococcus was significantly positively correlated with intestinal norank_f__Ruminococcaceae and Ruminococcus_torques_group in TIDM children. Moreover, in these children, differential genes in oropharyngeal and intestinal samples were enriched in metabolic pathways such as amino acid generation, fatty acid metabolism, and nucleotide sugar biosynthesis. Additionally, correlation analysis between the oropharyngeal/intestinal microbiome with laboratory tests showed significant correlations between several bacterial taxa in the oropharynx and intestines and glycated hemoglobin and C-peptide.
Conclusion
Unique microbial characteristics were found in the oropharynx and intestine in children with T1DM compared to healthy children. Positive correlations were found between changes in the relative abundance of oropharyngeal and gut microbiota in children with T1DM. Associations between the oropharyngeal/intestinal microbiota and laboratory investigations in children with T1DM suggest that the composition of the oropharyngeal and intestinal flora in children with T1DM may have some impact on glycemic control.
... The Illumina MiSeq platform (Illumina Inc., San Diego, CA, United States) was used for paired-end sequencing (2 × 300) of the PCR products. The raw sequence reads were quality-filtered and merged by FLASH (Tanja and Steven, 2011) before open-reference operational taxonomic unit (OTU) picking via UPARSE (Stackebrandt and Goebel, 1994;Edgar, 2013) and taxonomy classification through the SILVA 16S rRNA database (Wang, 2007). ...
This study aimed to explore whether Lactococcus G423 could improve growth performance and lipid metabolism of broilers by the modulation of gut microbiota and metabolites. A total of 640 1-day-old AA broilers were randomly divided into 4 groups [Control (CON), Lac_L, Lac_H, and ABX]. Average daily gain (ADG), average daily feed intake (ADFI), feed conversion ratio (FCR), breast muscle, thigh muscle, and abdominal fat pad were removed and weighed at 42 days of age. Serum was obtained by centrifuging blood sample from jugular vein (10 mL) for determining high-density lipoprotein (HDL), total cholesterol (TC), low-density lipoprotein (LDL), and triglyceride (TG) using ELISA. The ileal contents were harvested and immediately frozen in liquid nitrogen for 16S rRNA and LC–MS analyses. Then, the results of 16S rRNA analysis were confirmed by quantitative polymerase chain reaction (qPCR). Compared with the CON group, FCR significantly decreased in the Lac_H group (p < 0.05) in 1–21 days; ADG significantly increased and FCR significantly decreased in the Lac_H group (p < 0.05) in 22–42 days. 42 days weight body and ADG significantly increased in the Lac_H group (p < 0.05) in 42 days. Abdominal fat percentage was significantly decreased by Lactococcus G423 (p < 0.05), the high dose of Lactococcus G423 significantly decreased the serum of TG, TC, and LDL level (p < 0.05), and the low dose of Lactococcus G423 significantly decreased the serum of TG and TC level (p < 0.05). A significant difference in microbial diversity was found among the four groups. Compared with the CON group, the abundance rates of Firmicutes and Lactobacillus in the Lac_H group were significantly increased (p < 0.05). The global and overview maps and membrane transport in the Lac_L, Lac_H, and ABX groups significantly changed versus those in the CON group (p < 0.05). The results of LC–MS demonstrated that Lactococcus could significantly improve the levels of some metabolites (6-hydroxy-5-methoxyindole glucuronide, 9,10-DiHOME, N-Acetyl-l-phenylalanine, and kynurenine), and these metabolites were involved in four metabolic pathways. Among them, the pathways of linoleic acid metabolism, phenylalanine metabolism, and pentose and glucuronate interconversions significantly changed (p < 0.05). Lactococcus G423 could ameliorate growth performance and lipid metabolism of broilers by the modulation of gut microbiota and metabolites.
... nucleotide mismatches in primer matching. Sequences meeting these criteria were aligned with the SILVA database (Quast et al., 2013) and classified into identical operational taxonomic units (OTUs) with a 97% similarity threshold using UPARSE version 11 (Stackebrandt and Goebel, 1994;Edgar, 2013). Chimera sequences were removed in the clustering process and the most abundant sequence for each OTU was selected as a representative sequence. ...
Introduction
The Sanxingdui Site in Guanghan City, Sichuan Province, China, is one of the precious heritage sites of the ancient Chinese civilization. Archaeological work at Sanxingdui is of great significance in clarifying the origins and main contents of the ancient Shu culture and the Yangtze River civilization. Since the 1920s, archaeologists have conducted extensive excavations and research at the site, with particular attention given to the large number of ivory artifacts unearthed. However, the buried ivory is influenced by soil pH, temperature, humidity, and other physical and chemical factors, along with the potential impact of microbial activities that may lead to the corrosion and decomposition of ivory. By understanding the types and activities of microorganisms, appropriate measures can be taken to protect and preserve cultural relics.
Methods
Multi-point sampling of soil samples around the ivory of the three sacrificial pits at the Sanxingdui site was carried out, and strict aseptic operation was carried out during the sampling process. Subsequently, the microbial community structure and diversity in the buried ivory soil of Sanxingdui site were identified and analyzed by Illumina high-throughput sequencing technology.
Results
16S rRNA and internal transcribed spacer sequence analysis revealed significant differences in the soil microbial community structure among different sacrificial pits. The dominant bacterial phyla were the Proteobacteria, GAL15, Actinobacteriota, Bacteroidota, and Methylomirabilota. The dominant fungal phyla were Ascomycota, Mortierellomhcota, and Basidiomycota. Most dominant bacterial and fungal communities play an indispensable role in the ivory corrosion mechanism, promoting the decay and decomposition process through various means such as decomposing organic matter and producing acidic substances.
Discussion
It is particularly important to take a series of measures to control microbial activity to effectively protect ivory. Our preliminary study of the mechanism of action of microorganisms on ivory in a buried environment provides a scientific basis to prevent and protect against microbial degradation in ancient ivory unearthed in Sanxingdui. Following the research results, suitable antibacterial agents tailored to the preservation environment and microbial characteristics of ancient ivory can be prepared. Ensure that the selected antibacterial agents meet safety and effectiveness requirements to maximize protection against microbial degradation of ancient ivory.
... The values below 95-96% for ANI and 70% for dDDH confirmed that strains 74-4 T , 419-1.2 T , and 262-4 represented two novel species of the genera Lacticaseibacillus and Companilactobacillus [25][26][27][28]. ...
Three Gram-stain-positive bacterial strains were isolated from traditional Chinese pickle and characterized using a polyphasic taxonomic approach. Results of 16S rRNA gene sequence analysis indicated that strain 74-4T was most closely related to the type strains of Lacticaseibacillus suibinensis and Lacticaseibacillus suilingensis, having 99.9% and 100% 16S rRNA gene sequence similarities, respectively, and that strains 419-1.2T and 262-4 were most closely related to the type strains of Companilactobacillus heilongjiangensis, Companilactobacillus nantensis, Companilactobacillus huachuanensis, and Companilactobacillus nuruki, having 98.5–99.7% 16S rRNA gene sequence similarities. The phylogenomic trees indicated that strain 74-4T was related to the type strains of L. suibinensis and L. suilingensis, and that strains 419-1.2T and 262-4 were related to the type strains of C. heilongjiangensis, C. nantensis, C. huachuanensis, and Companilactobacillus zhachilii. The ANI and dDDH values between strain 74-4T and type strains of phylogenetically related species were less than 92.7% and 49.9%, respectively. The ANI and dDDH values between strains 419-1.2T and 262-4 and type strains of phylogenetically related species were less than 93.4% and 51.7%, respectively. Based upon the data of polyphasic characterization obtained in the present study, two novel species, Lacticaseibacillus salsurivasis sp. nov. and Companilactobacillus muriivasis sp. nov., are proposed and the type strains are 74-4T (= JCM 35890T = CCTCC AB 2022414T) and 419-1.2T (= JCM 35891T = CCTCC AB 2022413T), respectively.
... The barcode allowed zero mismatches, while up to two primer mismatches were permitted. Operational taxonomic units (OTUs) were clustered at a 97% similarity threshold, and chimeras were removed using UPARSE v7.1 software (Stackebrandt and Goebel, 1994;Edgar, 2013). More information on UPARSE can be found at http://drive5.com/uparse/. ...
Gut microbes are pivotal reference indicators for assessing the health status of animals. Before introducing artificially bred species into the wild, examining their gut microbe composition is crucial to help mitigate potential threats posed to wild populations. However, gut microbiological trait similarities between wild and artificially bred green turtles remain unexplored. Therefore, this study compared the gut microbiological characteristics of wild and artificially bred green turtles (Chelonia mydas) through high-throughput Illumina sequencing technology. The α-diversity of intestinal bacteria in wild green turtles, as determined by Shannon and Chao indices, significantly surpasses that of artificial breeding green turtles (p < 0.01). However, no significant differences were detected in the fungal α-diversity between wild and artificially bred green turtles. Meanwhile, the β-diversity analysis revealed significant differences between wild and artificially bred green turtles in bacterial and fungal compositions. The community of gut bacteria in artificially bred green turtles had a significantly higher abundance of Fusobacteriota including those belonging to the Paracoccus, Cetobacterium, and Fusobacterium genera than that of the wild green turtle. In contrast, the abundance of bacteria belonging to the phylum Actinobacteriota and genus Nautella significantly decreased. Regarding the fungal community, artificially bred green turtles had a significantly higher abundance of Fusarium, Sterigmatomyces, and Acremonium and a lower abundance of Candida and Rhodotorula than the wild green turtle. The PICRUSt2 analyses demonstrated significant differences in the functions of the gut bacterial flora between groups, particularly in carbohydrate and energy metabolism. Fungal functional guild analysis further revealed that the functions of the intestinal fungal flora of wild and artificially bred green turtles differed significantly in terms of animal pathogens-endophytes-lichen parasites-plant pathogens-soil saprotrophs-wood saprotrophs. BugBase analysis revealed significant potential pathogenicity and stress tolerance variations between wild and artificially bred green turtles. Collectively, this study elucidates the distinctive characteristics of gut microbiota in wild and artificially bred green turtles while evaluating their health status. These findings offer valuable scientific insights for releasing artificially bred green turtles and other artificially bred wildlife into natural habitats.
... FLASH [40] (1.2.11) software was used for splicing. UPARSE v7.1 [41,42] software was used to perform operational taxonomic unit (OTU) clustering on the concatenated quality control sequences according to a 97% similarity. In order to minimize the impact of sequencing depth on the subsequent alpha diversity analysis, the sequence number of all samples was flattened to 20,000 (sequence flattening is recommended). ...
The Songnen grassland is an important resource for livestock production in China. Due to the intensification of anthropogenic activities in recent years, vegetation degradation has worsened, and the salinization of grassland has become increasingly serious, which severely affects the sustainable development of grassland animal husbandry. In this study, organic fertilizer addition was carried out at saline-and-alkaline-degraded Songnen grassland sites with photovoltaic panels, and we investigated the effects of organic fertilizer treatments on the vegetation and soil bacteria in these areas. The results showed that both organic fertilizer treatments increased the community composition and diversity indices of plants (p < 0.05); they also had significant effects on soil electrical conductivity and rapidly available potassium (p < 0.05). In the dominant phylum of bacteria, the relative abundance of Firmicutes increased without adding organic fertilizer under the photovoltaic panel; the addition of organic fertilizer had a significant effect on the relative abundance of Firmicutes and Desulfobacterota (p < 0.05), reducing their relative abundance, respectively. There were differences in the number of bacteria at the genus level under different treatments compared to the control, with the highest enrichment of bacteria occurring at the OFE position, and a significant difference (p < 0.05) being found between the control and the other four groups at the genus level of g_norank_f_norank_o_Actinomarinales. Organic fertilizer had a significant effect on the bacterial Simpson diversity index, with the most significant increasing trend found in OFE (the front eaves of the photovoltaic panel in fertilization area). The results of a correlation analysis showed that pH, electrical conductivity, and total nitrogen were the main factors affecting the soil bacterial community.
... Then, the V4 region of the bacterial 16S rDNA gene was amplified using a pair of primers, 515F (5′-GTGCCAGCMGCCGCGG-3′) and 806R (5′-GGACTACHVGGGTWTCTAAT-3′). Operational taxonomic units (OTUs) with a similarity greater than or equal to 97%were clustered and analyzed for classification [51,52]. Bioinformatic analysis of the gut microbiota was done using Majorbio Cloud (https://cloud.majorbio.com, ...
The gut microbiota has become an essential component of the host organism and plays a crucial role in the host immune system, metabolism, and physiology. Nevertheless, our comprehension of how the fish gut microbiota contributes to enhancing nutrient utilization in the diet and improving host growth performance remains unclear. In this study, we employed a comprehensive analysis of the microbiome, metabolome, and transcriptome to analyze intestines of the normal control group and the antibiotic-treated model group of T. ovatus to investigate how the gut microbiota enhances fish growth performance and uncover the underlying mechanisms. First, we found that the growth performance of the control group was significantly higher than that of the antibiotic-treated model under the same feeding conditions. Subsequent multiomics analyses showed that the gut microbiota can improve its own composition by mediating the colonization of some probiotics represented by Lactobacillus in the intestine, improving host metabolic efficiency with proteins and lipids, and also influencing the expression of genes in signaling pathways related to cell proliferation, which together contribute to the improved growth performance of T. ovatus. Our results demonstrated the important contribution of gut microbiota and its underlying molecular mechanisms on the growth performance of T. ovatus.
... (3) samples were differentiated by barcode and primers, and sequence direction was adjusted with exact barcode matching and a 2-nucleotide mismatch allowance in primer matching. The optimized sequences were clustered into operational taxonomic units (OTUs) at a 97% sequence similarity level using UPARSE 7.1 (Stackebrandt and Goebel 1994;Edgar 2013). The most abundant sequence in each OTU was selected as a representative sequence. ...
Aims
Banana Fusarium wilt (Fusarium oxysporum f. sp. cubense tropical race 4) is a typical destructive soil-borne disease, which was the main limiting factor for the sustainable development of the banana industry worldwide. In banana production, soil physiochemical properties and soil microbiome were effectively affected the occurrence and spread of Fusarium wilt. However, there is still a lack of systematic research, particularly in exploring the correlation between the occurrence of banana Fusarium wilt and soil properties across various climates and soil types.
Methods
In this study we investigated the soil physicochemical properties, bacterial and fungal community composition, and pathogenic fungal abundance in 140 banana plantations which were affected by banana Fusarium wilt in Yunnan Province, China.
Results
The results showed that the abundance of soil-borne pathogenic fungi was positively correlated with total phosphorus, total nitrogen, organic matter, urease activity, annual precipitation, and the alpha diversity of bacterial and fungal communities. In contrast, it showed a significant negative correlation with the annual mean temperature. As the abundance of pathogen increased, numerous potential disease-suppressive bacterial genera (such as Rhodanobacter, Gemmatimonas, Novosphingobium) and soil-borne pathogenic fungal genera (such as Plectosphaerella, Nigrospora, Cyphellophora) also increased, and the co-occurrence network showed a higher modularization index.
Conclusions
The results enhance the understanding of the patterns of soil-borne pathogenic fungal population dynamics in banana plantations, which would provide evidence and guidance for reducing pathogenic fungal abundance and selecting beneficial microorganisms in banana production. Furthermore, this would provide a theoretical basis for sustainable prevention and control of banana wilt disease.
... Bacteria with relative abundance < 0.01% of the sample was classified as other categories, and bacteria with relative abundance > 5.00% was referred to as the dominant bacteria. Based on the OTUs information, alpha diversity indices including observed Chao1 richness, Shannon index and Simpson index were calculated with Mothur v1.30.1 [30]. In Alpha diversity analysis, Chao index refers to community richness, Shannon and Simpson indices refer to community diversity. ...
The epiphytic and endophytic bacteria play an important role in the healthy growth of plants. Both plant species and growth environmental influence the bacterial population diversity, yet it is inconclusive whether it is the former or the latter that has a greater impact. To explore the communities of the epiphytic and endophytic microbes in Camellia oleifera , this study assessed three representative C. oleifera cultivars from three areas in Hunan, China by Illumina high-throughput sequencing. The results showed that the diversity and species richness of endophytic microbial community in leaves were significantly higher than those of microbial community in the epiphytic. The diversity and species richness of epiphytic and endophytic microbes are complex when the same cultivar was grown in different areas. The C. oleifera cultivars grown in Youxian had the highest diversity of epiphytic microbial community, but the lowest abundance, while the cultivars grown in Changsha had the highest diversity and species richness of endophytic microbes in leaves. It was concluded that the dominant phylum mainly included Proteobacteria, Actinobacteriota and Firmicutes through the analysis of the epiphytic and endophytic microbial communities of C. oleifera . The species and relative abundances of epiphytic and endophytic microbial community were extremely different at the genus level. The analysis of NMDS map and PERMANOVA shows that the species richness and diversity of microbial communities in epiphytes are greatly influenced by region. However, the community structure of endophytic microorganisms in leaves is influenced by region and cultivated varieties, but the influence of cultivars is more significant. Molecular ecological network analysis showed that the symbiotic interaction of epiphytic microbial community was more complex.
... Operational taxonomic units (OTUs) with 97% similarity cutoff were clustered using UPARSE version 7.1, and chimeric sequences were identified and removed (Stackebrandt and Goebel, 1994;Edgar, 2013). The taxonomy of each OTU representative sequence was analyzed by RDP Classifier version 2.2 against the 16S rRNA database using confidence threshold of 0.7 (Wang et al., 2007). ...
Ageratina adenophora can enhance its invasive ability by using beneficial rhizosphere bacteria. Bacillus cereus is able to promote plant growth and provide a positive feedback effect to A. adenophora. However, the interaction between A. adenophora and B. cereus under the influence of native polyphagous insect feeding is still unclear. In this study, Eupatorium lindleyanum, a local species closely related to A. adenophora, was used as a control, aimed to compare the content of B. cereus in the roots of A. adenophora and rhizosphere soil after different densities of Aphis gossypii feeding, and then investigated the variations in the population of A. gossypii and soil characteristics after the addition of B. cereus. The result showed that B. cereus content in the rhizosphere soil and root of A. adenophora increased significantly under A. gossypii feeding compared with local plants, which also led to the change of α-diversity and β-diversity of the bacterial community, as well as the increase in nitrate nitrogen (NO3 –N) content. The addition of B.cereus in the soil could also inhibit the population growth of A. gossypii on A. adenophora and increase the content of ammonium nitrogen (NH4 ⁺-N) in the soil. Our research demonstrated that B. cereus enhances the ability of A. adenophora to resist natural enemy by increasing soil ammonium nitrogen (NH4 ⁺-N) and accumulating other beneficial bacteria, which means that rhizosphere microorganisms help invasive plants defend themselves against local natural enemies by regulating the soil environment.
... Concurring with Shalygin et al. (2017), our phylogenetic analyses based on the rbcLX gene sequences indicated that the topology of Phayaothrix did not belong to the described cyanobacterial genera and confirmed our taxonomic evaluation of the Phayaothrix clade based on the16S rRNA gene phylogenetic trees. The thresholds for prokaryotic genera and species separation are 94.5% and 98.7% similarities of the 16S rRNA gene sequences, respectively (Stackebrandt & Goebel 1994, Stackebrandt & Ebers 2006, Yarza et al. 2014. Other data such as phenotypic, genetic or environment supported the discrimination of genus/species levels. ...
In this study, novel Calothrix-like strains NUACC09 and NUACC10 were isolated from the surfaces of rocks in Phayao Lake, Thailand. Morphological, molecular and ecological comparisons were investigated to characterize the taxonomic status of these novel strains. Under the light microscope, morphological studies indicated that these two strains were morphologically similar to Calothrix but could be differentiated by production of a non-hyaline hair at the terminal end, a low degree of tapering, twisted or loop-forming filaments, a knotted growth form, intertwined trichomes and presenting more than one trichome within the single sheath. In the 16S rRNA and rbcLX gene phylogenetic tree analyses, our strains formed a monophyletic clade with former freshwater/terrestrial Calothrix-like taxa separating distantly from other Calothrix-like genera. Furthermore, low 16S rRNA gene sequence similarity (<94.9%) to the closely related genera and species delimitation analyses (PTP/bPTP, GMYC, ABGD and ASAP methods) indicated that this clade should be considered as a different cyanobacterial lineage. The phylogenetic tree and secondary structures (D1–D1′, V2, Box-B and V3 helix) based on 16S–23S rRNA ITS regions suggested that multiple species might be contained in this clade. Therefore, here, Phayaothrix was proposed as a novel cyanobacterial genus with Phayaothrix lacustris sp. nov. as the type species following the International Code of Nomenclature for algae, fungi and plants.
... UPARSE software (http://drive5.com/uparse/ (accessed on 11 January 2023), version 7.1) was used to group the sequences into amplicon sequence variants (ASVs) at 97% similarity [30,31], and chimeric sequences were removed. The RDP classifier [32] (http://rdp.cme.msu.edu/ ...
The use of green manure can substantially increase the microbial diversity and multifunctionality of soil. Green manuring practices are becoming popular for tobacco production in China. However, the influence of different green manures in tobacco fields has not yet been clarified. Here, smooth vetch (SV), hairy vetch (HV), broad bean (BB), common vetch (CV), rapeseed (RS), and radish (RD) were selected as green manures to investigate their impact on soil multifunctionality and evaluate their effects on enhancing soil quality for tobacco cultivation in southwest China. The biomass of tobacco was highest in the SV treatment. Soil pH declined, and soil organic matter (SOM), total nitrogen (TN), and dissolved organic carbon (DOC) content in CV and BB and activity of extracellular enzymes in SV and CV treatments were higher than those in other treatments. Fungal diversity declined in SV and CV but did not affect soil multifunctionality, indicating that bacterial communities contributed more to soil multifunctionality than fungal communities. The abundance of Firmicutes, Rhizobiales, and Micrococcales in SV and CV treatments increased and was negatively correlated with soil pH but positively correlated with soil multifunctionality, suggesting that the decrease in soil pH contributed to increases in the abundance of functional bacteria. In the bacteria–fungi co-occurrence network, the relative abundance of key ecological modules negatively correlated with soil multifunctionality and was low in SV, CV, BB, and RS treatments, and this was associated with reductions in soil pH and increases in the content of SOM and nitrate nitrogen (NO3−-N). Overall, we found that SV and CV are more beneficial for soil multifunctionality, and this was driven by the decrease in soil pH and the increase in SOM, TN, NO3−-N, and C- and N-cycling functional bacteria.
... The allowable mismatch number of the barcode was 0, and the maximum mismatch number of the primer was 2. Using UPARSE software (http:// drive5.com/uparse/, version 7.1) (Edgar, 2013), according to 97% OTU on the sequence of similarity clustering and eliminate chimeras (Stackebrandt and Goebel, 1994;Edgar, 2013). Species classification annotation was conducted on each sequence using the RDP classifier (http://rdp.cme.msu.edu/, ...
Introduction
Chrysanthemum morifolium Ramat. is a perennial herb in the Compositae family, often employed in traditional Chinese medicine due to its medicinal value. The planting of C. morifolium faces the challenges of continuous cropping, and intercropping is able to somewhat overcome the obstacles of continuous cropping.
Methods
In our study, we designed two different C. morifolium-maize intercropping patterns, including C. morifolium-maize narrow-wide row planting (IS) and C. morifolium-maize middle row planting (IM). Compared with monoculture, the agronomic traits, yield, active ingredients, soil physicochemical properties, soil enzyme activities, and rhizosphere soil microbial communities of C. morifolium and maize were measured under the two C. morifolium-maize intercropping patterns.
Results
The findings indicated that (1) Intercropping elevated the agronomic traits, yield, and active ingredients of C. morifolium, especially in C. morifolium-maize narrow-wide row planting pattern, which indicating that interspecific distance played an important role in intercropping system; (2) Intercropping enhanced soil physicochemical properties and enzyme activities of C. morifolium and maize; (3) Intercropping altered rhizosphere soil microbial communities of C. morifolium and maize, making microbial interrelationships more complex. (4) Intercropping could recruit a large number of beneficial microorganisms enrich in the soil, including Bacillus, Sphingomonas, Burkholderia-Caballeronia-Paraburkholderia, Chaetomium, and Ceratorhiza, which may increase the content of AN, NN, AvK, ExCa, AvCu, AvZn and other nutrients in soil and promoted the growth and quality of C. morifolium.
Discussion
In summary, intercropping with maize could promote the accumulation of beneficial microorganisms in the soil, thus improving the overall growing environment, and finally realizing the growth and improvement of C. morifolium.
... This discipline has a rich and intricate history, dating back to the 17 thcentury discovery of prokaryotes through invention and further enhancement of light microscopy [12]. This period may be considered as the genesis of the phenotype-based taxonomy of microorganisms, which eventually led to the evolution of modern polyphasic taxonomy [13][14][15]. These developments occurred in parallel with research progress in molecular biology of cells, microbial physiology, and biogeochemistry [16]. ...
Prokaryotes are ubiquitous in the biosphere, important for human health and drive diverse biological and environmental processes. Systematics of prokaryotes, whose origins can be traced to the discovery of microorganisms in the 17th century, has transitioned from a phenotype-based classification to a more comprehensive polyphasic taxonomy and eventually to the current genome-based taxonomic approach. This transition aligns with a foundational shift from studies focused on phenotypic traits that have limited comparative value to those using genome sequences. In this context, Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB) and Bergey's International Society for Microbial Systematics (BISMiS) play a pivotal role in guiding prokaryotic systematics. This review focuses on the historical development of prokaryotic systematics with a focus on the roles of BMSAB and BISMiS. We also explore significant contributions and achievements by microbiologists, highlight the latest progress in the field, and anticipate challenges and opportunities within prokaryotic systematics. Additionally, we outline five focal points of BISMiS that are aimed at addressing these challenges. In conclusion, our collaborative effort seeks to enhance ongoing advancements in prokaryotic systematics, ensuring its continued relevance and innovative characters in the contemporary landscape of genomics and bioinformatics.
... The samples were distinguished according to the barcode and primers at the rst and last ends of the sequences, and the sequences were adjusted based on the direction. The number of mismatches allowed by the barcode was 0, and the maximum number of primers mismatched was 2. Using UPARSE software (version 7.1), OTU clustering was performed on non-repetitive sequences (excluding single sequences) according to 97% similarity, and chimeras were removed during the clustering process to obtain OTU representative sequences [93][94]. All sample sequences were levelled by sequence pumping at the minimum number of sample sequences, and the average sequence coverage (Good's coverage) for each sample could still reach 99.09%. ...
As the most abundant group of mammals, rodents possess a very rich ecotype, which makes them ideal for studying the relationship between diet and host gut microecology. Zokors are specialized herbivorous rodents adapted to living underground. Unlike more generalized herbivorous rodents, they feed on the underground parts of grassland plants. There are two species of the genus Myospalax in the Eurasian steppes in China: one is Myospalax psilurus , which inhabits meadow grasslands and forest edge areas, and the other is M. aspalax , which inhabits typical grassland areas. How are the dietary choices of the two species adapted to long-term subterranean life, and what is the relationship of this diet with gut microbes? Are there unique indicator genera for their gut microbial communities? Relevant factors such as the ability of both species to degrade cellulose are not yet clear. In this study, we analysed the gut bacterial communities and diet composition of two species of zokors using 16S amplicon technology combined with macro-barcoding technology. We found that the diversity of gut microbial bacterial communities in M. psilurus was significantly higher than that in M. aspalax and that the two species of zokors possessed different gut bacterial indicator genera. Based on the results of Mantel analyses, the gut bacterial community of M. aspalax showed a significant positive correlation with the creeping-rooted type food, and there was a complementary relationship between the axis root type food and the rhizome type food dominated (containing bulb types and tuberous root types) food groups. Functional prediction based on KEGG found that M. psilurus possessed a stronger degradation ability in the same cellulose degradation pathway. Neutral modelling results showed that the gut flora of the M. psilurus has a wider ecological niche compared to that of the M. aspalax . This provides a new perspective for understanding how rodents living underground in grassland areas respond to changes in food conditions.
... The dDDH values between MAHUQ-54 T and Aquincola tertiaricarbonis L10 T and Leptothrix mobilis Feox-1 T were 25.3 and 20.8 %, respectively (Table S2). These ANI values and dDDH values are well below the species thresholds of 95-96 and 70 %, respectively, indicating that MAHUQ-54 T represents a novel species [17][18][19]. On the basis of dDDH results, ANI values and the results of phylogenetic analysis, it is evident that the isolated strain represents a novel species of the genus Aquincola. ...
A Gram-stain negative, aerobic, rod-shaped, motile and flagellated novel bacterial strain, designated MAHUQ-54 T , was isolated from the rhizospheric soil of eggplant. The colonies were observed to be light pink coloured, smooth, spherical and 0.2–0.6 mm in diameter when grown on R2A agar medium for 2 days. MAHUQ-54 T was able to grow at 15–40 °C, at pH 5.5–9.0 and in the presence of 0–0.5 % NaCl (w/v). The strain gave positive results for both catalase and oxidase tests. The strain was positive for hydrolysis of l -tyrosine, urea, Tween 20 and Tween 80. On the basis of the results of 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Aquincola and is closely related to Aquincola tertiaricarbonis L10 T (98.8 % sequence similarity) and Leptothrix mobilis Feox-1 T (98.2 %). MAHUQ-54 T has a draft genome size of 5 994 516 bp (60 contigs), annotated with 5348 protein-coding genes, 45 tRNA and 5 rRNA genes. The average nucleotide identity (ANI) and digital DNA–DNA hybridisation (dDDH) values between MAHUQ-54 T and its closest phylogenetic neighbours were 75.8–83.3 and 20.8–25.3 %, respectively. In silico genome mining revealed that MAHUQ-54 T has a significant potential for the production of novel natural products in the future. The genomic DNA G+C content was determined to be 70.4 %. The predominant isoprenoid quinone was ubiquinone-8. The major fatty acids were identified as C 16 : 0 , summed feature 3 (comprising C 16 : 1 ω7 c and/or C 16 : 1 ω6 c ) and summed feature 8 (comprising C 18 : 1 ω7 c and/or C 18 : 1 ω6 c ). On the basis of dDDH, ANI value, genotypic analysis, chemotaxonomic and physiological data, strain MAHUQ-54 T represents a novel species within the genus Aquincola , for which the name Aquincola agrisoli sp. nov. is proposed, with MAHUQ-54 T (=KACC 22001 T = CGMCC 1.18515 T ) as the type strain.
... The sequencing data were pretreated to remove chimeras from the datasets. After optimizing the sequences, the UPARSE 28 pipeline was used to generate an operational taxonomic unit (ASV) table 29 . The identity threshold to bin the sequences into ASVs was 97%, and the most abundant sequence from each ASV was selected as the representative sequence for that ASV. ...
Soil microbial communities play a crucial role in maintaining diverse ecosystem functions within the saline–alkali soil ecosystems. The current understanding of harnessing soil microbial communities to enhance the salinized soil environment is limited. Therefore, in this study, we collected various saline–alkaline soils from across the Inner Mongolia Hetao irrigation area. The soil chemical properties were analyzed, and the microbial diversity of bacteria and fungi was measured using Illumina MiSeq. The dynamic relationship between the soil microbial community and soil factors was analyzed using the ABT model, the co-occurrence network, and the structural equation model. The results indicated that electrical conductivity (EC) was the biggest driving force of various saline–alkaline soils, affecting the community structure of bacteria (22.80%) and fungi (21.30%). The soil samples were categorized into three treatment levels based on their EC values: the low-salinity group (L, EC: 0–1 ms/cm, n = 10), the medium-salinity group (M, EC: 1–2 ms/cm, n = 8), and the high-salinity group (H, EC > 2 ms/cm, n = 6). Significant differences were observed in the microbial diversity and community structure for the different saline-alkali soils ( p < 0.01). The network diagram illustrated a positive correlation between salinity and the number of network points, network edges, and modularity coefficient, but a negative relationship with the number of modules. The results demonstrated a negative correlation between microbial abundance and salinity–alkalinity, while revealing an enhanced interrelationship among species. Saline-alkali ions were identified as the primary and direct driving factors responsible for bacterial (12.36%) and fungal (22.92%) community dynamics in various saline–alkaline soils. The alterations in bacterial (12.36%) and fungal (22.92%) communities in various saline-alkali soils were primarily driven by saline-alkali ions, which served as the principal direct factors. The negative correlation between EC and SOM exhibited the highest magnitude, whereas the positive correlation between soil organic carbon and EC demonstrated the greatest strength. Therefore, it was further substantiated that EC played a pivotal role in shaping the distinct microbial communities in saline-alkali soils.
... Sequence alignment of the 16S rRNA gene showed that isolates P1 and M7 were closely related to B. aerius strain 24K and P. (Bacillus) aryabhattai strain B8W22, respectively. According to Stackebrandt and Goebel [46], two organisms with a DNA similarity of >97.5% are closely related at the species level. Interestingly, Bacillus produces various metabolites that have antibacterial effects, such as bacitracin [47], macrolactin [48], and bacilysin [49]. ...
Unexplored soil bacteria isolated from Muna Island, Southeast Sulawesi, Indonesia, provide a new source of active molecules serving as prospective antibacterial agents. In the present research, the antibacterial and antibiofilm activities of bacterial isolates obtained from Muna Island were evaluated. Based on the preliminary screening through the antagonism assay, 5 out of the 15 isolates exhibited various spectra of antibacterial activities. At a concentration of 80 mg/ml, metabolites extracted from the two selected isolates, M7 and P1 inhibited the growth of the five multidrug-resistant strains. These extracts exhibited minimum inhibitory concentration and minimum bactericidal concentration values of 312.5 μg/ml to more than 10,000 μg/ml. An analysis of the 16S rRNA sequences revealed that the corresponding isolates were closely related to Bacillus aerius strain 24K and Priestia (Bacillus) aryabhattai strain B8W22, with >97% similarity. Some genes involved in antibiotic biosynthesis, such as mlnA, baeR, srfA, dfnD, and bacD, were also present in the bacterial genome. Liquid chromatography-tandem mass spectrometry analysis of the most potent M7 extract showed that it contained several antibacterial compounds, such as cyclo(D-Pro-L-Tyr), marinoquinoline G, and rancinamycin Ib.
... The maximum mismatch ratio of overlap region is 0.2, and reads that could not be assembled were discarded; and (iii) samples were distinguished according to the barcode and primers, and the sequence direction was adjusted. Then, the optimized sequences were clustered into operational taxonomic units (OTUs) using UPARSE 7.1 (Stackebrandt and Goebel, 1994;Edgar, 2013) with 97% sequence similarity level. The most abundant sequence for each OTU was selected as a representative sequence. ...
Introduction
At present, the use of beneficial microorganisms to control cucumber Fusarium wilt is a widely used method, and the rhizosphere microecological reset is one of the mechanisms involved. However, how biocontrol strains reshape cucumber rhizosphere microecology remains to be further studied.
Methods
The composition changes of cucumber root exudates induced by biocontrol strain 1JN2, the microbial ecology of cucumber rhizosphere and the colonization ability of biocontrol strain 1JN2 in cucumber rhizosphere were analyzed through UHPLC-MS/MS analysis, Illumina high-throughput sequencing and SEM, respectively.
Results
First, cucumber plants treated with biocontrol Bacillus 1JN2 reduced the disease severity of Fusarium wilt by 60%. Significant changes in cucumber root exudates were found after 1JN2 inoculation and the contents of four amino acids including glutamine, tryptophan, glycine and glutamic acid were significantly increased. Second, It was found that the bacterial diversity in the rhizosphere of cucumber was significantly increased in both the strain treatment group and the amino acid mixture treatment group, The number of Bacillus was the largest in all dominant populations, exceeded 20% in all treatment groups. The bacteria of Hydrogenispora and Vicinamibacteria were significantly increased after treatment.
Discussion
Overall, the results demonstrated that amino acid substances in cucumber root exudates induced by biocontrol strain 1JN2 can shift the cucumber root microenvironment and prevent the occurrence of Fusarium wilt disease.
... The earlier published literature has shown that operational taxonomic units (OTUs) assigned to morphologically unidentifiable species are less frequently criticized and accepted to some extent [67,68]. The BIN system was developed to overcome these constraints [69]. ...
... Finally, the library was sequenced using a NovaSeq 6,000 SP Reagent Kit v1.5 (Illumina, United States). The similarity threshold for OTU clustering was set at 97% (Stackebrandt and Goebel, 1994). One dog in the CK group and one in the HG group failed the faecal sample quality control, resulting in only five beagles in each of the CK and HG groups for which results were available. ...
There is growing interest in the potential health benefits of probiotics for both humans and animals. The study aimed to investigate the effects of feeding the canine-derived probiotic Pediococcus acidilactici GLP06 to adult beagles by analysing the microbiome and metabolome. Twenty-four healthy adult beagles were randomly assigned to four groups. The CK group received a standard diet, while the three probiotic groups, the LG group (2 × 10⁸ CFU/day/dog), MG group (2 × 10⁹ CFU/day/dog), and HG group (2 × 10¹⁰ CFU/day/dog), received the standard diet supplemented with varying amounts of probiotics. The results show that, compared to the CK group, total antioxidant capacity was significantly increased in the MG and HG groups (p < 0.05), and superoxide dismutase and catalase were significantly increased in the HG group (p < 0.05). Compared to the CK group, malondialdehyde and blood urea nitrogen content were significantly decreased in the MG and HG groups (p < 0.05). Additionally, secretory immunoglobulin A activity was significantly increased in the HG group compared to the CK and LG groups (p < 0.05), and immunoglobulin G activity was significantly increased in the HG group compared to the CK, LG, and MG groups (p < 0.05). In addition, compared with the CK group, the abundance of Faecalitalea and Collinsella increased in the LG group, and the relative abundance of Tyzzerella and Parasutterella increased in the MG group. The α diversity and the relative abundances of beneficial bacteria (Faecalibacterium, Lachnospiraceae_NK4A1316, and Ruminococcaceae_UCG-005) were higher in the HG group than in the CK group. Furthermore, acetic acid content was significantly increased in the HG group compared to the CK, LG, and MG groups (p < 0.05). Butyric acid, isobutyric acid, and the total SCFA content were significantly increased in the HG group compared to the CK group (p < 0.05). Moreover, metabolome analysis revealed 111 upregulated and 171 downregulated metabolites in the HG group. In conclusion, this study presents evidence that supplementing with P. acidilactici GLP06 can have a positive impact on antioxidant activity, immunoproteins, SCFAs, and gut microbiota in adult beagles. These findings highlight the potential of probiotics as a dietary intervention to enhance gut health and overall wellbeing in companion animals.
A 28-day pesticide degradation experiment was conducted for broccoli (Brassica oleracea L. var. italica Planch) and pakchoi (Brassica chinensis L.) with three pesticides (chlorantraniliprole (CAP), haloxyfop-etotyl (HPM), and indoxacarb (IXB)) to explore the effects of biochar on pesticide environmental fate and rhizosphere soil diversity. Rice straw biochar (RB) was applied to soil at a 25.00 t·ha−1 dosage under greenhouse conditions, and its effects on the degradation of three pesticides in vegetables and in soil were investigated individually. Overall, RB application effectively facilitated CAP and HPM degradation in broccoli by 13.51-39.42% and in broccoli soil by 23.8-74.1%, respectively. RB application slowed the degradation of CAP, HPM and IXB in pakchoi by 0.00-57.17% and slowed the degradation of CAP in pakchoi by 37.32-43.40%. The results showed that the effect of RB application on pesticide degradation in crops and soil was related to biochar properties, pesticide solubility, plant growth status, and soil characteristics. Rhizosphere soil microorganisms were also investigated, and the results showed that biochar application may be valuable for altering bacterial richness and diversity. The effect of biochar application on pesticide residues in crops and soil was influenced by the growth status of crops at first, and the second influencing factor was pesticide characteristics. Our results suggested that biochar application in soil could reduce pesticide non-point source pollution, especially for highly soluble pesticides, and could affect soil microorganisms.
Rapid climate change in the Arctic is altering microbial structure and function, with important consequences for the global ecosystem. Emerging evidence suggests organisms in higher trophic levels may also influence microbial communities, but whether warming alters these effects is unclear. Wolf spiders are dominant Arctic predators whose densities are expected to increase with warming. These predators have temperature-dependent effects on decomposition via their consumption of fungal-feeding detritivores, suggesting they may indirectly affect the microbial structure as well. To address this, we used a fully factorial mesocosm experiment to test the effects of wolf spider density and warming on litter microbial structure in Arctic tundra. We deployed replicate litter bags at the surface and belowground in the organic soil profile and analyzed the litter for bacterial and fungal community structure, mass loss, and nutrient characteristics after 2 and 14 months. We found there were significant interactive effects of wolf spider density and warming on fungal but not bacterial communities. Specifically, higher wolf spider densities caused greater fungal diversity under ambient temperature but lower fungal diversity under warming at the soil surface. We also observed interactive treatment effects on fungal composition belowground. Wolf spider density influenced surface bacterial composition, but the effects did not change with warming. These findings suggest a widespread predator can have indirect, cascading effects on litter microbes and that effects on fungi specifically shift under future expected levels of warming. Overall, our study highlights that trophic interactions may play important, albeit overlooked, roles in driving microbial responses to warming in Arctic terrestrial ecosystems.
IMPORTANCE
The Arctic contains nearly half of the global pool of soil organic carbon and is one of the fastest warming regions on the planet. Accelerated decomposition of soil organic carbon due to warming could cause positive feedbacks to climate change through increased greenhouse gas emissions; thus, changes in ecological dynamics in this region are of global relevance. Microbial structure is an important driver of decomposition and is affected by both abiotic and biotic conditions. Yet how activities of soil-dwelling organisms in higher trophic levels influence microbial structure and function is unclear. In this study, we demonstrate that predicted changes in abundances of a dominant predator and warming interactively affect the structure of litter-dwelling fungal communities in the Arctic. These findings suggest predators may have widespread, indirect cascading effects on microbial communities, which could influence ecosystem responses to future climate change.
The use of algae as feedstock for industrial purposes, such as in bioethanol production, is desirable. During a search for new agarolytic marine bacteria, a novel Gram-stain-negative, strictly aerobic, and agarolytic bacterium, designated as TS8 T , was isolated from algae in the harbour of the island of Susak, Croatia. The cells were rod-shaped and motile. The G+C content of the sequenced genome was 38.6 mol%. Growth was observed at 11–37 °C, with 0.5–13 % (w/v) NaCl, and at pH 6.0–9.0. The main fatty acids were summed feature 3 (C 16 : 1 ω 6 c and/or C 16 : 1 ω 7 c ), summed feature 8 (C 18 : 1 ω 7 c and/or C 18 : 1 ω 6 c ), and C 16 : 0 . The main respiratory quinone was ubiquinone-8. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Analysis of 16S rRNA gene sequences indicated that the newly isolated strain belongs to the genus Catenovulum . Based on 16S rRNA gene sequence data, strain TS8 T is closely related to Catenovulum sediminis D2 T (95.7 %), Catenovulum agarivorans YM01 T (95.0 %), and Catenovulum maritimum Q1 T (93.2 %). Digital DNA–DNA hybridization values between TS8 T and the other Catenovulum strains were below 25 %. Based on genotypic, phenotypic, and phylogenetic data, strain TS8 T represents a new species of the genus Catenovulum , for which the name Catenovulum adriaticum sp. nov. is proposed. The type strain is TS8 T (=DSM 114830 T =NCIMB 15451 T ).
Cyanobacteria are ancient organisms that contribute significantly to primary production in aquatic ecosystems. Although they are a group of microbes present in a wide range of environments, their diversity on anthropogenic substrates, namely microplastics, is still largely unknown. In the present study, we describe a new genus and species of cyanobacteria from the Nodosilineaceae family. Strains were isolated from foam microplastic particles obtained from beach sediments facing the Singapore Strait. This species is morphologically similar to the polyphyletic, cosmopolitan Leptolyngbya spp.; however, it forms an independent clade with 16S rRNA phylogeny and has a unique 16S–23S internal transcribed spacer secondary structure. To date, no cyanobacteria have been isolated and cultured from the surfaces of microplastic particles. Using a polyphasic approach combining morphological, phylogenetic and ecological traits, we describe a new genus and species Sphaerothrix gracilis. The presence of certain cyanobacteria rafting on microplastic surfaces can potentially indicate a long‐distance transport into new ecosystems with implications on toxicity and biodiversity.
In 2018, Nouioui et al. proposed that Bifidobacterium coryneforme was a later synonym of Bifidobacterium indicum on the basis of the digital DNA-DNA hybridization (dDDH) value (85.0%) between B. coryneforme LMG 18911T and B. indicum LMG 11587T. However, in the study of Scardovi et al. (1970), the type strains of B. indicum and B. coryneforme only exhibited 60% DNA-DNA hybridization value. In the present study, the genomes of B. coryneforme CGMCC 1.2279T, B. coryneforme JCM 5819T, B. indicum JCM 1302T, B. indicum CGMCC 1.2275T, B. indicum DSM 20214T, B. indicum LMG 27437T, B. indicum ATCC 25912T, B. indicum KCTC 3230T, B. indicum CCUG 34985T, were sequenced, and the taxonomic relationship between B. coryneforme and B. indicum was re-evaluated. On the basis of the results presented here, (i) ATCC 25912 and DSM 20214 deposited by Vittorio Scardovi are two different strains; (ii) the type strain of B. indicum is ATCC 25912T (= JCM 1302T = LMG 27437T = CGMCC 1.2275T = KCTC 3230T), and not DSM 20214 (= BCRC 14674 = CCUG 34985 = LMG 11587); (iii) B. coryneforme and B. indicum represent two different species of the genus Bifidobacterium; (iv) strain DSM 20214 (= BCRC 14674 = CCUG 34985 = LMG 11587) belongs to B. coryneforme.
Plastic pollution is a ubiquitous contemporary problem that demands to be addressed with urgency. Microorganisms that can degrade plastics may hold the key to resolving this problem by providing genetic and metabolic pathway knowledge on plastic degradation. In this study, soil samples were taken from Bago
City Sanitary Landfill in Negros Occidental to isolate bacteria capable of degrading plastic pollutants. For 60 days, 5 bacterial isolates were cultured in minimal medium with pieces of UV- and autoclave (AC)-sterilized PET films. After 60 days, the film reduction analysis showed that isolate PT1 significantly degraded 9.29% of
the UV-treated PET films when compared with the control, uninoculated PET films. Through molecular and biochemical characterization, the isolate was identified as Rhodococcus gordoniae PT1. The other bacterial isolates that showed growth on minimal medium with plastic as the sole carbon source were identified as
Acinetobacter wuhouensis, Acinetobacter bohemicus, and Streptomyces ruber. The scanning electron microscopy analysis revealed the presence of structural changes, such as cracks and holes, on the bacteria inoculated films, indicating plastic degradation. The ability of these bacteria to degrade plastic provides a foundation for bioremediation, green chemistry, and bioengineering, offering a potential solution for eradicating tough pollutants from the environment. However, the potential pathogenicity of certain isolates needs careful considerations before applying these bacteria for bioremediation and bioengineering. Finally, this is the first study to identify plastic-degrading bacteria in Bago City, Negros Occidental, and the first to describe the plastic degrading potentials of the identified species.
To reduce pesticide pollution and promote sustainable agricultural development in China, we designed a pilot-scale biofilter system to treat residual imidacloprid wastewater in an orchard. The biofilter system demonstrated a high rate of removal of imidacloprid from the biodegradation wastewater, with removal rates from the outlet exceeding 99% at different concentrations of pesticides. Among environmental factors, imidacloprid concentration at the inlet and biomixture significantly affected the activity of imidacloprid-degrading bacteria. The dominant microbial communities during the stable operation of the biofilter system included Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes at the phylum level and Bacillus, Methylobacter, and unclassified_f__Microbacteriaceae at the genus level. In future initiatives to improve biofilter performance and applicability, increasing attention should be paid to the dominant microbial communities, the number of biofilter units, and important environmental factors. Orchard workers in China should improve the existing treatment of residual pesticide wastewater to mitigate agricultural non-point source pollution.
A Gram-stain-negative, aerobic, rod-shaped, motile, flagellated bacterial strain, designated as CAU 1639T, was isolated from the tidal flat sediment on the Yellow Sea in the Republic of Korea. Growth of the isolate was observed at 20–37 °C, at pH 5.0–10.5 and with 0–7% (w/v) NaCl. The genomic DNA G + C content was 60.8%. Phylogenetic analysis, grounded on 16S rRNA gene sequencing, revealed that strain CAU 1639T was closely related to species within the genus Roseibium. It shared the highest similarity with Roseibium album CECT 5095T, followed by Roseibium aggregatum IAM 12614T and Roseibium salinum Cs25T, with 16S rRNA gene sequence similarity ranging from 98.0–98.4%. It was observed that the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values ranged between 72.5–79.5 and 20.0–22.9%, respectively. The polyphasic taxonomic analysis reveals that strain CAU 1639T represents a novel species in the genus Roseibium with the proposed name Roseibium sediminicola sp. nov. The type strain is CAU 1639T (= KCTC 82430T = MCCC 1K06081T).
DNA-DNA hybridization (DDH) has been used as the gold standard in prokaryote taxonomy, but it is labor-intensive and prone to experimental errors. The development of high-throughput DNA sequencing technologies has greatly reduced the cost of genome sequencing, resulting in increased availability of microbial genomes. Traditional taxonomic methods, such as DDH, are being challenged by the rapid development of genomic metrics. Overall genome relatedness indices (OGRIs) have been developed to replace DDH. The present chapter describes the OGRI that has been developed as well as their interpretation for defining new taxonomic ranks.
Modern-day microbial taxonomists are embracing the inclusion of microbial genomic taxonomy in the declaration of new microbial species. With the advancement of molecular techniques and the development of new bioinformatic tools, the current shift in thought and application of taxonomic methods is inevitable. Unlike nomenclature, which is guided by a set of rules and recommendation, there is no formal regulation for methods to be used in microbial systematics, and hence, no clear set of characteristics are defined to propose a novel species. Over the years, scientists have adapted to the evolving trends of microbial taxonomic methods. In this chapter, we as practicing microbial taxonomists try to give our perspectives on the key features that may be considered for the declaration of new microbial species.
This study examined the fermentation dynamics, bacterial community composition and bacterial β -carotene synthesis in alfalfa that was ensiled for 3, 15, 45 and 90 days without additives (CON), or with a chemical agent (propionic acid, PA); or a combination of PA and squalene, SQPA). The results showed that silage treated with PA had a lower ( P < 0.01) pH value than the CON silage in the early ensiling phase (3–15 days). Meanwhile, silage treated with PA had the highest contents of lactic acid, acetic acid and PA after 90 days of ensiling ( P < 0.01). The β -carotene in alfalfa was lost seriously in the initial ensiling phase (3 days) and epiphytic Pantoea agglomerans with the ability to produce β -carotene became extinct. With the extension of ensiling time, the loss of β -carotene was alleviated in all silages. PA and SQPA not only lowered bacterial diversity and simplified bacterial networks but also facilitated the emergence of new β -carotene-producing bacteria. The metabolic function prediction indicated that β -carotene synthesis tended to decrease initially and subsequently increase during ensiling. Furthermore, the variance of enzymes involved in the bacterial synthesis of β -carotene in silages was influenced by PA, SQPA and ensiling time. In summary, the impact of solely adding PA demonstrated superior effects on the fermentation quality of alfalfa silage compared to the effects observed with SQPA. Throughout the ensiling of alfalfa, the succession of different β -carotene-producing bacteria resulted in fluctuations in the levels of β -carotene.
The primary endosymbionts of aphids are maternally inherited bacteria
that live only within specialized host cells. Phylogenetic analysis of
the 16S ribosomal DNA sequences of aphid endosymbionts reveals that they
are a monophyletic group with a phylogeny completely concordant with
that of their hosts, implying long-term cospeciation. Here we show that
rates of base substitution are similar in the 16S ribosomal DNA of
different endosymbiont lineages. In addition, we calibrate these rates
by assigning age estimates for ancestral aphid hosts to the
corresponding endosymbionts. The resulting rate estimates (1-2% per 50
Ma) are among the most reliable available for prokaryotes. They are very
near values previously conjectured by using more tenuous assumptions for
dating divergence events in eubacteria. Rates calibrated using dates
inferred from fossil aphids imply that Asian and American species of the
aphid tribe Melaphidina diverged by the early Eocene; this result
confirms an earlier hypothesis based on biogeographic evidence. Based on
these rate estimates, the minimum age of this endosymbiotic association
and the age of aphids as a whole is estimated at 160-280 Ma.
16S rRNA (genes coding for rRNA) sequence comparisons were conducted with the following three psychrophilic strains: Bacillus globisporus W25T (T = type strain) and Bacillus psychrophilus W16AT, and W5. These strains exhibited more than 99.5% sequence identity and within experimental uncertainty could be regarded as identical. Their close taxonomic relationship was further documented by phenotypic similarities. In contrast, previously published DNA-DNA hybridization results have convincingly established that these strains do not belong to the same species if current standards are used. These results emphasize the important point that effective identity of 16S rRNA sequences is not necessarily a sufficient criterion to guarantee species identity. Thus, although 16S rRNA sequences can be used routinely to distinguish and establish relationships between genera and well-resolved species, very recently diverged species may not be recognizable.
The primary structures of the 16S rRNAs of Bacillus anthracis, Bacillus cereus, Bacillus mycoides, and Bacillus thuringiensis were determined by using the reverse transcription-dideoxy sequencing method. All of the strains exhibited very high levels of sequence similarity (greater than 99%) that were consistent with the close relationships shown by previous DNA hybridization studies. The sequences of B. anthracis Sterne and B. cereus emetic strain NCTC 11143 were found to be identical for a continuous stretch of 1,446 bases and differed from the sequence of B. cereus NCDO 1771T (T = type strain) by only a single nucleotide. The 16S rRNA sequences of B. mycoides and B. thuringiensis differed from each other and from the sequences of B. anthracis and B. cereus by four to nine nucleotides.
This chapter discusses the deoxyribonucleic acid (DNA) reassociation and ribonucleic acid (RNA) hybridization of bacterial nucleic acids. The elucidation of the structure and the physical properties of deoxyribonucleic acid (DNA) and ribonucleic acids (RNAs) has enabled investigators to compare directly the sequence similarities in these molecules from one organism with those from another. These comparisons, DNA reassociation or RNA hybridization experiments, are measurements of the pairing of two DNA fragments or the pairing of an RNA molecule with a fragment of DNA. The specific pairings are between the base pairs adenine (A) and thymine (T) [or uracil (U) in RNA] and between guanine (G) and cytosine (C). The final success of the methods and procedures described in this chapter depends upon the initial growth of the bacterial cells and the isolation of DNA or RNA from them. Although techniques for following the growth of bacterial cultures are beyond the scope of this chapter, their importance cannot be overemphasized. Many organisms are fastidious and grow very slowly or to a low turbidity, others tend to die very rapidly after reaching stationary phase, while others may enter a sporulation phase.
Genetic diversity among 15 strains of Fibrobacter succinogenes and F. intestinalis was evaluated by comparative 16S rRNA sequencing, by estimation of genomic DNA similarity, and by restriction endonuclease digestion patterns. The previous division of the genus into two genetically well-resolved species (F. succinogenes and F. intestinalis) was confirmed by the additional comparative studies. All measures of genomic relatedness were consistent. The two species were related at approximately 91 to 93% 16S rRNA sequence similarity and less than 20% genomic DNA similarity. F. succinogenes subsp. elongata was found to comprise three subgroups related at ca 97% 16S rRNA sequence similarity; although subspecies status would be phylogenetically justifiable, difficulties in phenotypic distinction of these subgroups contraindicate formation of additional subspecies. Analysis of all pairwise comparisons showed that 50% DNA-DNA pairing corresponded to approximately 99% 16S rRNA sequence similarity.
Associations with cytoplasmically inherited microorganisms are fundamental to the ecology and reproductive biology of many insects. Molecular phylogenetics now provides a window into the previously obscure history of these associations. This approach has recently yielded striking findings for two cases: the mutualistic endosymbionts of aphids and relatives, and some of the cytoplasmically inherited organisms that induce reproductive abnormalities in various arthropods. These examples provide useful reference points for future extensions of molecular phylogenetic methods to other prokaryote-eukaryote associations.
DNA-DNA hybridization is a reliable method for determining the phylogenetic relationship between bacterial strains The hybridization kinetics for DNA from different slowly-growing mycobacteria were measured optically in a spectrophotometer. The results indicate that M. tuberculosis and M. bovis belong to one species. M. avium and M. intracellulare are two species, but some serotypes, now designated M. intracellulare, actually belong to M. avium.
Species of Enterobacter and Serratia were examined for deoxyribonucleic acid relatedness to Klebsielleae, to atypical erwiniae, and to other members of Enterobacteriaceae. Deoxyribonucleic acid hybridization and then hydroxyapatite chromatography was the technique used to assess relatedness. Strains of Enterobacter cloacae formed two separate hybridization groups that correlate with the presence or absence of yellow pigment. Pigmented E. cloacae were 75-100% related, but they were only 40-50% related to unpigmented strains. Conversely, unpigmented strains were 70% or more related but were only 40-50% related to the pigmented strains. Both pigmented and unpigmented E. cloacae were 40-45% related to Enterobacter aerogenes and klebsiellae, and 20-30% related to Serratia species and Enterobacter hafniae. Atypical erwiniae were highly related to E. cloacae. Serratia marcescens strains formed one closely related group. Serratia liquefaciens strains formed a single, more disperse, relatedness group, as did isolates of Serratia rubidaea. These species were related throughout a substantial portion of their genomes. A group of lysine-positive "Citrobacter-like" strains were 40-50% related to Serratia species. Only four E. hafniae strains were tested. Two of these were highly related, while the other two were only 50% related to the reference strain. Enterobacter hafniae was only 15-20% related to other Enterobacteriaceae.
The potential of ribosomal (r) RNA and the encoding genes (rDNA) to elucidate natural relationships has been dramatically extended by improved sequencing approaches and the application of polymerase chain reaction. Sequence information on 16S and 23S rRNA/DNA from 69 strains of 53 Streptomyces species allows determination of regions that can be used as target sites for diagnostic probes, and for amplification and sequencing primers. To generate phylogenetic trees, sequence similarities are converted into distance values. The topologies of the trees based on different parts of the molecule are compared among each other and to the numerical phenotypic clustering of the strains.
Bacterial evolution is a topic that 10 years ago was little more than pseudoscience. Today, because of the capacity to determine and compare macromolecular sequences, the study of bacterial evolution is transforming the science of microbiology. Many hundreds of bacterial species have been characterized in terms of partial or complete ribosomal ribonucleic acid sequences, which permit the construction of a comprehensive phylogenetic tree. This phylogeny is of obvious value to the evolutionary biologist. It not only provides a framework within which to understand the evolution of bacterial phenotypes and the general nature of evolutionary process in the microbial world, but also allows one to approach the problems of cellular evolution and the relationship between physical changes in the planet and the evolutionary responses to them. The tree also has considerable predictive and organizational value for microbiology as a whole, affecting and changing the ways in which microbiologists interpret and design experiments as well as their overall perception of the field and its relationship to the other biological disciplines. The bacteria in actuality comprise two separate primary kingdoms, the eubacteria and the archaebacteria, no more related to one another than to eucaryotes. The eubacteria constitute about 10 major groups (the equivalent of eucaryotic phyla); the archaebacteria consist of at least five. The two kingdoms are very different, not only in general molecular phenotype but in the ways in which they evolve. The phylogenetic distribution of phenotypes in both kingdoms suggest that all procaryotes have ultimately arisen from thermophilic ancestry. There seems to exist a clear relationship between the rate at which bacteria evolve and the type of evolution they undergo. A rapid evolutionary course results in a highly altered phenotype, in a sense a damaged phenotype. Both this rate and the accompanying quality of evolutionary change seem to be mirrored in the changes that occur in ribosomal ribonucleic acids and presumably other molecular chronometers.
This paper constructs a temporal scale for bacterial evolution by tying ecological events that took place at known times in the geological past to specific branch points in the genealogical tree relating the 16S ribosomal RNAs of eubacteria, mitochondria, and chloroplasts. One thus obtains a relationship between time and bacterial RNA divergence which can be used to estimate times of divergence between other branches in the bacterial tree. According to this approach,Salmonella typhimurium andEscherichia coli diverged between 120 and 160 million years (Myr) ago, a date which fits with evidence that the chief habitats occupied now by these two enteric species became available that long ago.
The median extent of divergence betweenS. typhimurium andE. coli at synonymous sites for 21 kilobases of protein-coding DNA is 100%. This implies a silent substitution rate of 0.7–0.8%/Myr—a rate remarkably similar to that observed in the nuclear genes of mammals, invertebrates, and flowering plants. Similarities in the substitution rates of eucaryotes and procaryotes are not limited to silent substitutions in protein-coding regions. The average substitution rate for 16S rRNA in eubacteria is about 1%/50 Myr, similar to the average rate for 18S rRNA in vertebrates and flowering plants. Likewise, we estimate a mean rate of roughly 1%/25 Myr for 5S rRNA in both eubacteria and eucaryotes.
For a few protein-coding genes of these enteric bacteria, the extent of silent substitution since the divergence ofS. typhimurium andE. coli is much lower than 100%, owing to extreme bias in the usage of synonymous codons. Furthermore, in these bacteria, rates of amino acid replacement were about 20 times lower, on average, than the silent rate. By contranst, for the mammalian genes studied to date, the average replacement rate is only four to five times lower than the rate of silent substitution.
The effect of mismatched base pairs on the thermal stability of renatured DNA · DNA duplexes was determined by specific alkali deamination of deoxycytosine residues to deoxyuridine residues. After annealing with unaltered DNA, the effect of the resulting G · U pairs on thermal stability was measured. The measurements of were made optically or by dissociation of filter- or hydroxylapatite-bound duplexes. The results suggest an effect such that 1 % G · U pairs reduces the thermal stability by about 2.2 °C. Considering the available data, an estimate is suggested for the effect of mismatching in heteroduplexes formed by naturally occurring DNA in which mutations have accumulated.
The effect of depurination and chain scission on the thermal stability of DNA · DNA duplexes was studied. Escherichia coli DNA was subjected to limited depurination followed by alkaline hydrolysis at the points of purine loss. These modified single-strands were annealed alone or in the presence of excess unmodified DNA. The thermal stability of the annealed duplexes was measured in three ways to permit estimation of the effect of the changes on the stability of the DNA double strands. The reduction in thermal stability is linearly related to the percentage of lesions and the slope of this relationship is approximately the same for depurination and for chain scission.
M. avium and M. intracellulare are difficult to distinguish by means of biochemical tests and by means of numerical taxonomy. DNA-DNA hybridization confirms that these species are different but indicates that some serovars of M. intracellulare actually belong to the species M.avium, viz.: serovars 4, 5, 6 and 8. This corresponds to results obtained with sensitin tests on guinea-pigs. The status of strains belonging to serovar 9 is uncertain. The two strains investigated in this study were closely related to, but not identical with M. scrofulaceum serovar 41.
The DNA-DNA homology percentages obtained in this study indicate M. smegmatis, M. phlei, M. fortuitum, M. peregrinum, M. senegalense, M. farcinogenes, M. chelonei, M. parafortuitum, M. vaccae, M. diernhoferi and M. aurum are separate species. Taxonomically there is no justification for the designation M. fortuitum complex, and M. peregrinum should be revived as an independent species. The type strains of M. parafortuitum, M. vaccae, M. aurum and the non-valid M. diernhoferi are so distinct from each other that they should not be combined.
Comparative sequence analysis of in vitro-amplified 16S rRNA genes of Thiosphaera pantotropha GB17T (T = type strain) and Paracoccus denitrificans LMG 4218T revealed identical 16S rRNA primary structures for the two organisms. The level of overall DNA similarity of Thiosphaera pantotropha GB17T and P. denitrificans DSM 65T is 85%, as determined by quantitative DNA-DNA hybridization. Therefore, we propose the transfer of Thiosphaera pantotropha to P. denitrificans. The closest relative of Thiosphaera pantotropha and P. denitrificans is Thiobacillus versutus, as revealed by comparative 16S rRNA sequence analysis. These organisms are members of the alpha subclass of the Proteobacteria. Within this subclass, Thiosphaera pantotropha, P. denitrificans, and Thiobacillus versutus form a phylogenetic group with Rhodobacter sphaeroides, Rhodobacter capsulatus, and "Erythrobacter longus."
Untersuchungen iiber Bacterien IV
- F Cohn
Cohn, F. 1876. Untersuchungen iiber Bacterien IV. Beitr. Biol. Pfl
Deoxyribonucleic acid relationships between dif-ferent serovars of Mycobactenurn avium, Mycobactenum intracel-lulare and Mycobactenurn scrofulaceum
- I Baess
Baess, I. 1983. Deoxyribonucleic acid relationships between dif-ferent serovars of Mycobactenurn avium, Mycobactenum intracel-lulare and Mycobactenurn scrofulaceum. Acta Pathol. Microbiol
herpriifung der taxonomischen Stellung von Bacillus anthracis mit Hilfe der DNA Hybridisierungs Technik
- G Spaeth
Spaeth, G. 1989. herpriifung der taxonomischen Stellung von
Bacillus anthracis mit Hilfe der DNA Hybridisierungs Technik.
Ph.D. thesis. University Giessen, Giessen, Germany.
- F Cohn
Cohn, F. 1876. Untersuchungen iiber Bacterien IV. Beitr. Biol. Pfl.
Heft 2:249-277.
DNA reassociation and RNA hybridization of bacterial nucleic acids
- J L Johnson
Johnson, J. L. 1985. DNA reassociation and RNA hybridization of
bacterial nucleic acids. Methods Microbiol. 28:33-74.