Fig 3 - uploaded by Murray Wolinsky
Content may be subject to copyright.
Rank abundance plots of each model for the noncontaminated soil. Species are ranked in order from most abundant to least abundant.
Source publication
The complexity of soil bacterial communities has thus far confounded effective measurement. However, with improved analytical methods, we show that the abundance distribution and total diversity can be deciphered. Reanalysis of reassociation kinetics for bacterial community DNA from pristine and metal-polluted soils showed that a power law best des...
Similar publications
Agriculture has marked impacts on the production of carbon dioxide (CO(2)) and consumption of methane (CH(4)) by microbial communities in upland soils-Earth's largest biological sink for atmospheric CH(4). To determine whether the diversity of microbes that catalyze the flux of these greenhouse gases is related to the magnitude and stability of the...
Citations
... Soil microorganisms were highly important components and the most active constituents in the terrestrial soil system and played an indispensable role in soil formation and development, organic matter transformation, ecosystem balance, soil environmental purification and bioremediation (Gans et al., 2005). The results from the current study showed that although all sampling sites were located in the Hetao irrigation area, and the vegetation was S. glauca in all cases, the microbial characteristics exhibited extremely significant differences. ...
Exploring the bacterial community in the S. glauca rhizosphere was of great value for understanding how this species adapted to the saline-alkali environment and for the rational development and use of saline-alkali soils. In this study, high-throughput sequencing technology was used to investigate the diversity characteristics and distribution patterns of soil bacterial communities in the rhizosphere of S.glauca-dominated communities in the Hetao Irrigation Distract, Inner Mongolia, China. The relationships among bacterial characteristics, soil physicochemical properties and vegetation in four sampling sites were analyzed. The soil bacterial communities in the rhizosphere of S. glauca-dominated communities were mainly composed of 16 phyla (i.e., Proteobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Chloroflexi, Acidobacteria, Firmicutes, Planctomycetes, Deinococcus-Thermus, Verrucomicrobia, Saccharibacteria, Cyanobacteria, Nitrospirae, JL-ETNP-Z39, Parcubacteria and Chlorobi), and these populations accounted for more than 99% of the total bacterial community. At the genus level, the main bacterial communities comprised Halomonas, Nitriliruptor, Euzebya and Pelagibius, which accounted for 15.70% of the total bacterial community. An alpha diversity analysis indicated that the richness and diversity of rhizosphere soil bacteria differed significantly among the sampling sites, and the bacterial richness and diversity indices of severe saline-alkali land were higher than those of light and moderate saline-alkali land. The principal component analysis (PCA) and linear discriminant analysis effect size (LEfSe) showed significant differences in the species composition of the rhizosphere soil bacterial community among different sampling sites. A correlation analysis showed that the number of bacterial species exhibited the highest correlation with the soil water content (SWC). The richness and evenness indices were significantly correlated with the SWC and SO42–, K⁺ and Mg²⁺ concentrations. The electrical conductivity (EC), soluble ions (Na⁺, CO32– + HCO3–, K⁺, Ca²⁺, Mg²⁺, and SO4²⁺), SWC and vegetation coverage (VC) were the main drivers affecting the changes in its community structure. The bacterial community in the rhizosphere of S. glauca enhanced the adaptability of S. glauca to saline-alkali environment by participating in the cycling process of nutrient elements, the decomposition of organic matter and the production of plant growth regulating substances. These results provided a theoretical reference for further study on the relationship among rhizosphere soil microorganisms and salt tolerance in halophytes.
... Deceans et al. (2006) report that 360,000 animal species dwell in soil. Also, nearly 1010 bacterial cells are present in 10 g of soil (Gans et al. 2005). These organisms are vital to sustaining both soil and a wider ecosystem and are important for the production of food and fiber in addition to regulating other services like controlling the emission of greenhouse gases, purifying water, and nutrient cycling. ...
Soil erosion is a major concern that needs to be addressed for the health of an ecosystem. It is a primary constraint to agriculture, affecting the yield, water quality at the source, and soil health. It is often a result of anthropogenic activities like deforestation, unhealthy irrigation and agricultural practices and overgrazing, etc., and leads to degradation of the environment. Soil erosion is a threat of significant magnitude that needs to be addressed in regions of large agricultural productivity like Asia underlining the need for mitigation measures. Structural interventions like check dams, silt traps, etc. are extensively used to deter soil erosion. However, these interventions are not integral to the natural environment and adversely affect the ecosystem. This study reviews the various biogeotechnological methods to control soil erosion and conserve the soil. Biological interventions like vegetative cover on slopes have long been practiced to control soil erosion in select zones. Biogenic additives to soil that improve the resistance of soil against soil erosion need detailed investigation. In line with this observation, this study will review biogenic stabilizers like vegetative cover, biopolymers, and biochar and their efficacy in controlling soil erosion. The effect of this biogenic stabilizer against soil erosion caused by wind and water will be discussed in detail. These methods do not only help in controlling soil erosion but also improve soil health and promote vegetative growth. These soil additives offer environment-friendly, carbon–neutral/carbon-negative, and sustainable alternatives to structural interventions that are used to control soil erosion. They will improve soil health which in turn will lead to increased agricultural productivity and alleviate hunger and will help in conserving soil and end desertification (SDG 2 and 15).
... Soil microorganisms, particularly bacteria, are highly plentiful and varied, exerting significant influence in agricultural environments by aiding in nutrient cycling, upholding soil integrity, and enhancing plant development (Gans et al., 2005). Specific bacteria capable of promoting plant growth offer plants mechanisms to resist stress. ...
Beneficial bacteria that promote plant growth can shield plants from negative effects. Yet, the specific biological processes that drive the relationships between soil microbes and plant metabolism are still not fully understood. To investigate this further, we utilized a combination of microbiology and non-targeted metabolomics techniques to analyze the impact of plant growth-promoting bacteria on both the soil microbial communities and the metabolic functions within ramie (Boehmeria nivea) tissues. The findings indicated that the yield and traits of ramie plants are enhanced after treatment with Bacillus velezensis (B. velezensis). These B. velezensis strains exhibit a range of plant growth-promoting properties, including phosphate solubilization and ammonia production. Furthermore, strain YS1 also demonstrates characteristics of IAA production. The presence of B. velezensis resulted in a decrease in soil bacteria diversity, resulting in significant changes in the overall structure and composition of soil bacteria communities. Metabolomics showed that B. velezensis significantly altered the ramie metabolite spectrum, and the differential metabolites were notably enriched (P < 0.05) in five main metabolic pathways: lipid metabolism, nucleotide metabolism, amino acid metabolism, plant secondary metabolites biosynthesis, and plant hormones biosynthesis. Seven common differential metabolites were identified. Correlation analysis showed that the microorganisms were closely related to metabolite accumulation and yield index. In the B. velezensis YS1 and B. velezensis Y4-6-1 treatment groups, the relative abundances of BIrii41 and Bauldia were significantly positively correlated with sphingosine, 9,10,13-TriHOME, fresh weight, and root weight, indicating that these microorganisms regulate the formation of various metabolites, promoting the growth and development of ramie. Conclusively, B. velezensis (particularly YS1) played an important role in regulating soil microbial structure and promoting plant metabolism, growth, and development. The application of the four types of bacteria in promoting ramie growth provides a good basis for future application of biological fertilizers and bio-accelerators.
... The rank abundance plots offer a unified perception of the underlying ecological rules governing microbial diversity and abundance in a microbial ecology community (McGill et al., 2007;Prosser et al., 2007). However, because of the extensive complexity of these bacterial communities, accompanied by the inability to culture the vast majority of bacteria, the work necessary to obtain rank abundance plots is challenging (Curtis et al., 2006;Gans et al., 2005). Although 16S rRNA genes are widely used to characterize the structure and composition of microbial communities, having multiple copies often results in over-estimation of certain bacterial taxa, which lowers the ability to effectively enumerate bacterial community using bacterial species abundance distributions (Doroghazi and Buckley, 2008;Schloss and Handelsman, 2006;Sloan et al., 2007). ...
A R T I C L E I N F O Keywords: Personalized soil management Rhizobial diversity rpoB amplicon sequencing Conservation agriculture Tillage and cover crop Machine learning model Indigenous rhizobia A B S T R A C T Conservative agricultural management strategies pursue long-term ecological benefits through practices such as no-tillage, cover crop, and inherent soil properties management. Farmers, however, are often hesitant to adopt such practices due to lack of experience, initial expense, and concern for low crop productivity. Overcoming this barrier requires novel approaches, such as effectively managing the soil microbiome to attain high productivity at a low cost, especially in a semi-arid region. To study the potential of conservation agriculture, we investigated components of soil bacterial community and rhizobial diversity in long-term experimental cotton fields divided into conventional tillage monoculture systems with winter fallow (CT) and no-tillage with mixed cover crop (M-NT) system on the Texas High Plain (THP). We conducted next-generation amplicon sequencing targeting rpoB gene with collected soil samples from different soil managements and seasons. Our research revealed that although CT had significantly greater bacterial diversity and species richness than the M-NT management, rhizobial diversity and species richness were higher in M-NT than in CT management. Both bacterial and rhizobial diversity and richness were greater in summer than in fall. The abundance of the order Rhizobiales was consistently high in M-NT than in CT fields in both seasons. Soil management altered the dominant rhizobial genus associated with cotton production systems; Rhizobium and Pararhizobium dominated M-NT management, while Bradyrhizobium and Sinorhizobium were dominant under CT management. These outcomes suggest that incorporating legumes into a cover crop in this semi-arid cotton-growing region can initiate beneficial changes to the dynamics of the indigenous rhizobial assemblage. The high prediction accuracy of our machine learning model using bacterial community data classifying the managements as CT or M-NT validates the possibilities of a strong underlying relationship between soil management and the bacterial diversity in the soil.
... Soil, a living entity on earth (Sabale et al., 2019), is a product of microbial as well as macrobial life, and has within it a diverse ecosystemrepresented by a vast diversity and density of microbial communiites living in their own micro-environments in the soil. It is estimated that each gram of soil harbors more than 10 7 of prokaryotic cells with a phylogenetic diversity ranging in thousands of microbial taxa (Gans et al., 2005;Roesch et al., 2007). The ability of soil to function as a living environment for humans, plants, animals, and microorganisms is known as soil health (Lehmann et al., 2020). ...
The study of the whole of the genetic material contained within the microbial populations found in a certain environment is made possible by metagenomics. This technique enables a thorough knowledge of the variety, function, and interactions of microbial communities that are notoriously difficult to research. Due to the limitations of conventional techniques such as culturing and PCR-based methodologies, soil microbiology is a particularly challenging field. Metagenomics has emerged as an effective technique for overcoming these obstacles and shedding light on the dynamic nature of the microbial communities in soil. This review focuses on the principle of metagenomics techniques, their potential applications and limitations in soil microbial diversity analysis. The effectiveness of target-based metagenomics in determining the function of individual genes and microorganisms in soil ecosystems is also highlighted. Targeted metagenomics, including high-throughput sequencing and stable-isotope probing, is essential for studying microbial taxa and genes in complex ecosystems. Shotgun metagenomics may reveal the diversity of soil bacteria, composition, and function impacted by land use and soil management. Sanger, Next Generation Sequencing, Illumina, and Ion Torrent sequencing revolutionise soil microbiome research. Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)'s third and fourth generation sequencing systems revolutionise long-read technology. GeoChip, clone libraries, metagenomics, and metabarcoding help comprehend soil microbial communities. The article indicates that metagenomics may improve environmental management and agriculture despite existing limitations.Metagenomics has revolutionised soil microbiology research by revealing the complete diversity, function, and interactions of microorganisms in soil. Metagenomics is anticipated to continue defining the future of soil microbiology research despite some limitations, such as the difficulty of locating the appropriate sequencing method for specific genes.
... Selective inoculation of root microbiomes with growth-promoting microbes have also been shown to improve crop production [14][15][16]. Some of the more common microbial inoculation methods to confer stress tolerance include inoculation of the plant or seed via immersion [17], or mixing inoculum directly into the soil [18]. ...
Increasing soil salinity and/or sodicity is an expanding problem in the Northern Great Plains (NGP) of North America. This study investigated the impact of phytoremediation on the soil microbiome and if changes, in turn, had positive or negative effects on plant establishment. Amplicon sequencing and gas chromatograph/mass spectrometer analysis compared root metabolites and microbial composition of bulk vs. rhizosphere soils between two soil types (productive and saline/sodic). Beta-diversity analysis indicated that bacterial and fungal communities from both the bulk and rhizosphere soils from each soil type clustered separately, indicating dissimilar microbial composition. Plant species also influenced both root-associated bacterial and fungal communities with separate clustering of operational taxonomic units (OTUs) identified. Canonical correlation analysis (CCA) found a clear association between specific soil characteristics and soil types. Bacterial and fungal OTUs from productive soil were correlated with greater %Ca Sat, %H Sat, and potassium (ppm), especially for OTUs differentially enriched in productive soil. Both bacterial and fungal OTUs from saline/sodic soil are associated with increased Ca (ppm), soil pH, %Na Sat and CEC. Metabolite analysis showed that kochia (Bassia scoparia) roots from the saline/sodic soil had a 4.4-fold decrease in pantothenate accumulation (p = 0.004). Moreover, two endophytic bacterial isolates, a Bacillus spp. and a previously uncultured halophile, isolated from creeping foxtail (Alopecurus arundinaceus) grown in saline/sodic soil and used as buckwheat (Fagopyrum esculentum) seed inoculants, significantly increased seed germination by >30% and vigor index by 0.2 under osmotic stress (0.2 M NaCl) (p < 0.05). This study revealed the importance of soil, root-associated, and endophytic microbiomes. Using native microbes as seed inoculants may help in establishment and growth of species used for phytoremediation of saline/sodic soil.
... Quantity of microorganisms was determined as colony-forming units (CFU) per 1 g of dry soil (Carter, Gregorich, 2007). The studies conducted using this method allow observation of the most active organotrophs, nitrifiers, diazotrophs, the populations of soil fungi and yeast-like fungi, and changes of their abundance in the soil (Gans et al., 2005;Furtak, Gajda, 2018). ...
... Considering the main microbial groups inhabiting soil, bacteria have been the focal point of most studies, as they dominate soils with about 10 3 -10 6 per gram of soil [11]. However, fungal and archaeal groups are also important, with most studies showing their ubiquity in the soil [12]. ...
South Africa is a semi-arid country in need of soil conservation methods for sustainable agroecosystem practices. Over time, researchers have worked extensively on the plant growth beneficial effects of fungi. However, archaeal groups in the soil and rhizosphere of different plants are under-studied. The impact of soil edaphic factors on the community structure of archaeal and fungal groups in the maize rhizosphere is the focus of this research. This will confirm the hypothesis that environmental factors have a significant impact on the plant–soil rhizobiome. To achieve this objective, a shotgun metagenomics approach was used to analyze maize rhizosphere and bulk soils collected from North West and Gauteng provinces of South Africa. Our findings revealed that both the maize rhizosphere and bulk soils have several archaeal and fungal phyla in common. Besides, Ascomycota (30‒51%), Thaumarchaeota (14‒26%), Euryarchaeota (19‒29%), and Crenarchaeota (8‒12%) have significantly dominated the maize rhizosphere and surrounding bulk soils. In comparison, genera such as Nitrosopumilus (Ls-18.32%, Lc-16.25%; Rs-15.45%, Rc-11.47%), Candidatus Nitrososphaera (Ls-15.29%, Lc-13.37%; Rs-10.53%, Rc-8.29%), Cenarchaeum (Ls-8.84%, Lc-8.16%; Rs-7.63%, Rc-5.38%), Chaetomium (Ls-25.15%, Lc-23.05%; Rs-14.83%, Rc-6.29%), and Neurospora (Ls-2.09%, Lc-1.95%; Rs-1.05%, Rc-0.99%) were significantly higher in maize rhizosphere soils compared to bulk soils (p < 0.05). Diversity indices showed that the archaeal and fungal composition were significantly different across samples with the presence of unclassified groups that could indicate the possibility of novel organisms in the sampling areas. The forward selection of soil edaphic factors predicted N–NH4, pH, and organic matter as the major contributing factors to the variation in the fungal and archaeal communities. To fully exploit the advantages possessed by these species, it is necessary to better understand the main environmental factors driving microbial assemblages of the soil microbiome. In addition, mapping out a culture-based method to unveil the unclassified groups could assist in the discovery of biotechnologically important archaeal and fungal groups for sustainable plant growth.
... Tanah supresif layu fusarium dicirikan dengan tanah yang didominasi sejumlah mikrob fungsional melalui mekanisme tertentu yang menjadikan tanah sehat (healthy soils) dan menopang kehidupan tanaman (Yuan et al. 2021). Bakteri fungsional merupakan salah satu kelompok mikrob tanah dengan populasi paling beragam dan melimpah yang bertindak sebagai indikator kesehatan tanah, baik itu menguntungkan (beneficial microbes) maupun merugikan (deleterious microbes) (Gans et al. 2005). ...
Fenomena tanah supresif telah banyak dikaji sebagai metode pengendalian penyakit tanaman alami di lapangan dan dicirikan dengan banyaknya sejumlah mikrob fungsional yang mampu menekan populasi patogen. Penelitian ini bertujuan mengetahui dan membandingkan komposisi bakteri fungsional pada tanah supresif dan kondusif layu fusarium. Metode penelitian terdiri atas pengambilan sampel tanah di lapangan, isolasi bakteri fungsional dari sampel tanah supresif (TS) dan kondusif (TK), penghitungan populasi dan jenis bakteri, penapisan berdasarkan keamanan hayati, dan karakterisasi bakteri fungsional dalam menekan Fusarium oxysporum. Hasil penelitian menunjukkan bahwa populasi bakteri pada TS lebih tinggi dibandingkan TK, khususnya bakteri toleran panas dan Pseudomonas kelompok fluorescent. Hal ini didukung dengan tingginya nilai keanekaragaman bakteri fungsional pada TS (H’ 3.70 > 3) dibandingkan TK yang tergolong sedang (1 < H’ 2.07 < 3), dengan sebaran bakteri fungsional tergolong hampir merata dan tidak ditemukan adanya dominansi jenis tertentu pada TS maupun TK. Persentase bakteri nonpatogenik pada TS lebih tinggi dibandingkan TK, masing-masing 51% dan 23%. Bakteri tersebut berpotensi sebagai plant growth promoting bacteria (PGPB) dengan memproduksi IAA atau melarutkan fosfat saja, masing-masing 24% dan 10% pada TS, sedangkan pada TK masing-masing 14% dan 29%. Hanya bakteri yang berasal dari tanah supresif yang mampu memproduksi IAA sekaligus melarutkan fosfat dengan persentase sebanyak 48%.
... Soil environment has a multifaceted biological system (Gans, Wolinsky, and Dunbar 2005) with 1,000,000 species in a 10 g sample (Young and Crawford 2004). The first step of biosphere's development is biogenesis of soil, which involves nutrient recycling and the creation of soil. ...
