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Response curves of selected bacterial orders towards pH. Each line represents the predicted abundance changes along the measured pH gradient, based on predictions derived from multinomial regression models. A detailed version of this graph including the 30 most abundant orders is available as Supplementary Material Figure S4.
Source publication
Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils de...
Contexts in source publication
Context 1
... regression models revealed multiple responses of bacterial orders to soil pH. To better understand the complex relationship of single bacterial groups and soil pH, we applied multinomial regression models on the 30 most abundant orders of the dataset (Supplementary Material Figure S6). Four general Figure 3. Relative abundances of key enzymes in grassland and forest. ...
Context 2
... subgroup 3, Frankiales, Corynebacteriales), (2) increase in abundance with increasing pH (acidobacterial subgroup 6, Gaiellales, Acidimicrobiales, Propionibacteriales), (3) narrow pH range with high abundance (Rhizobiales, Rhodospirillales), and (4) relatively constant abundance across pH range (Bacillales, Gemmatimonadales, Sphingobacteriales) (Fig. 6). In their publication on niche theory, Austin and Smith 37 described pH as a direct physiological gradient acting on organisms, resulting in unimodal, or skewed unimodal response curves restricted by growth limiting conditions at one end, and competition at the other end. This is supported by our observation of few highly abundant ...
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... This predominance of deterministic processes driving bacterial community composition in grasslands was already demonstrated by Guo et al. [41]. The strong effect of pH on bacterial community composition is also well known [49,107]. As found by Navrátilová et al. [70], Proteobacteria and Actinobacteria are dominant in the Čertoryje grassland, but we also found Verrucomicrobia as a codominant phylum. ...
Background
Grasslands provide fundamental ecosystem services that are supported by their plant diversity. However, the importance of plant taxonomic diversity for the diversity of other taxa in grasslands remains poorly understood. Here, we studied the associations between plant communities, soil chemistry and soil microbiome in a wooded meadow of Čertoryje (White Carpathians, Czech Republic), a European hotspot of plant species diversity.
Results
High plant diversity was associated with treeless grassland areas with high primary productivity and high contents of soil nitrogen and organic carbon. In contrast, low plant diversity occurred in grasslands near solitary trees and forest edges. Fungal communities differed between low-diversity and high-diversity grasslands more strongly than bacterial communities, while the difference in arbuscular mycorrhizal fungi (AMF) depended on their location in soil versus plant roots. Compared to grasslands with low plant diversity, high-diversity plant communities had a higher diversity of fungi including soil AMF, a different fungal and soil AMF community composition and higher bacterial and soil AMF biomass. Root AMF composition differed only slightly between grasslands with low and high plant diversity. Trees dominated the belowground plant community in low-diversity grasslands, which influenced microbial diversity and composition.
Conclusions
The determinants of microbiome abundance and composition in grasslands are complex. Soil chemistry mainly influenced bacterial communities, while plant community type mainly affected fungal (including AMF) communities. Further studies on the functional roles of microbial communities are needed to understand plant-soil-microbe interactions and their involvement in grassland ecosystem services.
... Bulk density reflects soil biophysical properties such as texture, water content, porosity, and mineralogy that drive microbial community structure and function (19,53,54,118,119). Patterns in the relationships between these variables and the soil microbiome can be complex at global scales (19), and our findings are to our knowledge the first to report a global-scale relationship between bulk density and the distribution of genes encoded by the soil microbiome. ...
Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes—more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.
IMPORTANCE
We address a critical gap in our understanding of soil microorganisms and their functions, which have a profound impact on our environment. We analyzed 1,512 global soils with advanced analytics to create detailed genetic profiles (fingerprints) of soil microbiomes. Our work reveals novel patterns in how microorganisms are distributed across different soil environments. For instance, we discovered shifts in microbial potential to acquire nutrients in relation to soil acidity, as well as changes in stress responses and potential greenhouse gas emissions linked to soil structure. We also identified soils with putative high activity that had unique genomic characteristics surrounding resource acquisition, plant-microbe interactions, and fungal activity. Finally, we observed that closely related microorganisms tend to respond in similar ways to changes in their surroundings. Our work is a significant step toward comprehending the intricate world of soil microorganisms and its role in the global climate.
... Nonetheless, a number of publications have documented contrasting patterns, describing the prevalence of microbial K-strategists when forests are changed to grasslands. Specifically, in comparison with forests, grasslands had lower labile carbon contents and greater relative abundances of K-bacteria, such as Acidobacteria, Alphaproteobacteria and Gemmatimonadetes (Kaiser et al. 2016;Wang et al. 2019b). The transition from forest to grassland might also keep the microbial community unchanged due to the similar soil carbon pool between forest and grassland (Zimmermann et al. 2010;Dieleman et al. 2013). ...
Background and aims
The forest–grassland transect in the Greater Khingan Mountains, located in the southern edge of the permafrost region in Eurasia, is more vulnerable to climatic changes than other terrestrial ecosystems. The impacts of climate-induced vegetation conversion on soil microbial ecological strategies are still under debate, and the underlying mechanisms are not known.
Methods
Soil microbial community composition was investigated using 16SrRNA gene amplicon sequencing. The activities of soil enzymes responsible for organic matter mineralization, along with soil physicochemical properties and vegetation characteristics were examined in parallel. The dominance of microbial r-strategy was predicted by a variety of physiological and phylogenetic traits, including the r-/K-strategists ratio, the ribosomal RNA (rrn) operon copy number of bacterial community, saprotrophic/ectomycorrhizal fungi ratio, and the stoichiometric ratio between enzymes hydrolyzing simple (cellobiose and oligosaccharide) and complex (cellulose and protein) organic compounds.
Results
Overall, microbial r-strategy relevant traits were higher in grasslands than in forests. Within forests, when vegetation changed from conifers to broadleaf forests from northeast to southwest, the labile carbon fraction of soil organic matter increased, stimulating the prevalence of soil microbial community r-strategy. Across grassland sites, the r-strategy relevant traits decreased towards the warm, dry site, due to the declined C and N availability.
Conclusion
This study implied that, under future warm conditions, forest ecosystems would be associated with an r-shifted soil microbial community and thus face a potential risk of carbon loss; whereas in grassland ecosystem, soil microbial community would be shifted towards a K-spectrum and might reduce the risk of carbon loss.
... Microbial communities, which are important ecosystem indicators for coastal zones, are crucial for promoting material flow and energy flow (Yi et al., 2020). Microbial abundance and diversity can measure the stability of bacterial community structure (Kaiser et al., 2016). In the current study, it was discovered that while microbial community abundance and diversity varied significantly between various topographic features, such as marine manholes and river inlets, overall species composition and diversity remained largely at the same level. ...
... Bacterial communities are essential to soil ecology, especially the forestry ecosystem [1,2]. They can degrade organic and inorganic compounds in the soil into soluble substances that trees can use for their development [3]. ...
... The diversity of soil bacteria differed between forest types, soil depths, and slope positions [7]. Bacterial community structure also showed a significant difference among land use types, with a higher diversity in grassland soils than forest soils [1]. For croplands, soil bacterial communities were more influenced by winter than summer [8]. ...
Pollutants can exist in the soil for a long time and alter the bacterial community. Using lubricants to prevent the wear of chainsaw blades is necessary for thinning activities and wood harvesting. We investigated the influences of soil contamination with chainsaw lubricants on soil bacterial communities. Bio-oil, mineral oil, and recycled oil were scattered on each treatment to investigate variations in soil bacterial structure during treated periods using the Illumina MiSeq sequencing platform. The results obtained were 5943 ASVs, 5112 ASVs, and 6136 ASVs after treatment at one month, six months, and twelve months, respectively. There was a significant difference in Shannon and Simpson indices between treatments and controls. A total of 46 bacterial genera with an average relative abundance of more than 1.0% were detected in all soil samples. Massilia was the most common genus detected in control at one month, with an average relative abundance of 14.99%, while Chthoniobacter was the most abundant genus detected in bio-oil, mineral oil, and recycled oil treatments at one month, with an average relative abundance of 13.39%, 14.32%, and 10.47%, respectively. Among the three chainsaw lubricants, bio-oil and mineral oil had fewer impacts than recycled oil. The abundances of several functional bacteria groups in the bio-oil treatment were higher than in other treatments and controls. Our results indicated that different chainsaw lubricants and their time of application affected the soil bacterial community composition.
... pH is one of the key indexes influencing soil's microbial community diversity; the closer the soil value is to a neutral pH (pH = 7), the greater the bacterial diversity is [38]. In the present study, the soil pH was the lowest under the T6 treatment and the highest under the CK1 treatment. ...
The return of agricultural waste to the field is one of the most effective strategies of increasing crop yield, improving the soil’s physicochemical properties, and improving the soil rhizosphere environment. In the present study, sheep manure (SM), cow manure (CM), tail vegetable (TV), mushroom residue (MR), and corn straw (CS) were used as raw materials, and no fertilization (CK1) and local commercial organic fertilizer (CK2) treatments were used as controls. Eight composts were set up using specific mass ratios of different compost materials. After fermentation, field experiments were conducted to determine the cabbage yield, soil’s physicochemical properties, and soil rhizosphere conditions. The eight composts increased the soil organic matter and nutrient contents significantly. Among the eight fermentation formulas, T6 (CM:CS:TV:SM = 1:1:2:6), T7 (MR:CS:TV:SM = 1:1:2:6), and T8 (CM:MR:CS:TV:SM = 1:1:1:2:5) were relatively effective. Therefore, high-throughput sequencing was performed on T6, T7, T8, CK1, and CK2. T6, T7, and T8 exhibited increased relative abundance of Proteobacteria, Actinomycetes, and Firmicutes, while the Acidobacteria abundance was decreased. In addition, Ascomycota’s and Basidiomycetes’ relative abundance decreased, and the oil chytrid and mortierella increased. The microbial community structure was affected significantly by pH, electrical conductivity, available potassium, available nitrogen, and organic matter. In general, the three composts increased yield by improving the soil’s physicochemical properties, fertility, and microbial community structure. Among them, T6 had the most significant effect and is the optimal formula for use as a local organic cabbage fertilizer, and it could facilitate sustainable agricultural development.
... phyla that showed high frequency in other forest soils worldwide, such as Chloroflexi and Gemmatimonadetes (Hartmann et al., 2012(Hartmann et al., , 2014Urbanová et al., 2015;Kaiser et al., 2016), were less represented here. These relative abundances corresponded to intermediate values of the ecological clusters defining bacterial phylotypes with preference for acidic, low productive soils . ...
... Changes in aggregation and biologically active organic C and N fractions could also be important steps toward a shift in soil microbial community structure (Yu et al., 2021). Characterization of soil properties with long-term land use change is needed across a diversity of farms throughout a region, as farm management and inherent soil properties can have a huge influence on outcomes (Franzluebbers & Poore, 2021;Kaiser et al., 2016). ...
Background
Soil organic C and N data from privately managed pastures in the southeastern United States are relatively scant.
Methods
A paired‐farm approach was deployed to determine how a variety of soil health parameters related to nutrient and water cycling might be altered under grazed, botanically diverse perennial pastures compared with annual monoculture croplands in three Major Land Resource Areas of the southeastern United States.
Results
Soil stability index averaged 0.64 and 0.91 mm mm ⁻¹ under cropland and grazed pasture, respectively, suggesting that pastures had a more stable soil surface that was resistant to erosion and allowed rapid water infiltration. Surface‐soil organic C and N fractions (i.e., total, particulate, and mineralizable fractions at 0–10 cm depth) were greater under pasture than under cropland. Across locations, root‐zone enrichments (0–30 cm depth) of organic C and N fractions were greater under pasture than under cropland. Within locations, root‐zone enrichment of total soil N was greater ( p < 0.05) under pasture than under cropland in the Blue Ridge (2.87 vs. 1.10 Mg N ha ⁻¹ , respectively) and the Piedmont (2.80 vs. 2.10 Mg N ha ⁻¹ ), but not in the Blackland Prairie (2.40 vs. 2.12 Mg N ha ⁻¹ ).
Conclusions
This study provides evidence that rotationally grazed, perennial grasslands can store more soil organic C and N and improve soil surface stability conditions compared with neighboring croplands producing commodity feed grains for feedlot finishing.
... It is crucial to emphasize that soil bacterial communities are highly responsive to environmental changes. Prior studies highlight the pivotal role of environmental factors, particularly soil pH, in shaping soil bacterial communities' composition and diversity [36,37]. In our study, we observed a clear correlation between soil pH and the bacterial community. ...
Ecological restoration has notably impacted microbe and soil characteristics in abandoned open pit mines, especially in alpine regions. Yet, the adaptive responses of microbial communities in the initial years of mine site restoration remain largely unexplored. This study endeavors to offer a thorough comprehension of soil properties and microbial dynamics during the initial phases of alpine mining land reclamation. It places emphasis on physicochemical properties and microbial community composition and evaluates the feasibility of phytoremediation, along with proposing subsequent measures. Our study employs spatial sequence instead of time-sequenceal sequence to investigate early-stage changes in soil microbes and physicochemical properties in alpine mining land reclamation. We used high-throughput sequencing for the 16S rRNA amplicon study. Over time, soil physicochemical properties improved noticeably. Soil pH shifted from neutral to alkaline (7.04–8.0), while soil electrical conductivity (EC) decreased to 77 μS·cm−1 in R_6a. Cation exchange capacity (CEC) initially decreased from R_2a (12.30–27.98 cmol·kg−1) and then increased. Soil organic matter increased from 17.7 to 43.2 g·kg−1 over time during mine reclamation and restoration. The dominant bacterial community consisted of Proteobacteria (33.94% to 52.09%), Acidobacteriota (4.94% to 15.88%), Bacteroidota (6.52% to 11.15%), Actinobacteriota (7.18% to 9.61%), and Firmicutes (4.52% to 16.80%) with varying relative abundances. Gene annotation of sequences from various reclamation years revealed general function prediction, translation, ribosome structure, cell wall/membrane/envelope biogenesis, nucleotide translocation, and metabolism, along with other related functions. Mine reclamation improved soil fertility and properties, with the R_6a treatment being the most effective. Starting in the 2nd year of reclamation, the effective phosphorus content and the dominance of microbial bacteria, notably the Bacillus content, decreased. Firmicute fertilization promoted phosphorus and bacterial growth. In conclusion, employing a blend of sequencing and experimental approaches, our study unveils early-stage enhancements in soil microbial and physicochemical properties during the reclamation of alpine mining areas. The results underscore the beneficial impacts of vegetation restoration on key properties, including soil fertility, pore structure, and bacterial community composition. Special attention is given to assessing the effectiveness of the R_6a treatment and identifying deficiencies in the R_2a treatment. It serves as a reference for addressing the challenges associated with soil fertility and microbial community structure restoration in high-altitude mining areas in Qinghai–Tibet. This holds great significance for soil and water conservation as well as vegetation restoration in alpine mining regions. Furthermore, it supports the sustainable restoration of local ecosystems.
... Previous studies run in the same experimental site after fertilization treatments ceased show that NP input reduced plant richness, this being partly driven by invasion of the exotic grass Melita minutiflora (de Mello et al. 2014, Silveira et al. 2021, and that soil chemistry, organic matter dynamics and soil microbial community differed between treatments (Silveira et al. 2021;Pompermaier et al. 2022). These differences in soil may partly explain the long-term effects on the vegetative and reproductive parts of plants, since soil microbiota release several enzymes involved in the cycle of several nutrients such as C and N, P, S (Falkowski et al. 2008;Kaiser et al. 2016). Yet, while N deposition is known to be a dominant factor driving leaf C:N ratio change (Sheng et al. 2021), and C leaf content and AA pollen content of our study species were altered, N leaf content remained similar, and changes in the C:N leaf ratio was not statistically different (note that for other plant species from the same experimental plot, significant C:N leaf ratio were (18) detected, unpublished data). ...
Human activities have substantially increased soil nutrient availability during the past decades, affecting plant community composition and plants' nutritional content. Several amino acids found in pollen, the main source of larval diet for bees, affect the development, health, and behaviour of this important group of pollinators. A better understanding of the consequences of global changes on pollen amino acid content can help explain and predict future impacts on bee populations and diversity. This is particularly relevant in regions that are highly exposed to fertilizers due to their importance for global food production, such as the Brazilian savannas (Cerrado), where soils are mostly dystrophic. Here, we use a long-term controlled fertilization experiment conducted in Cerrado and demonstrate that even after 10 years since the last fertilization addition, effects were still detectable on leaf and pollen chemical content. More specifically, pollen amino acid content of Pavonia rosa-campestris (Malvaceae), a species known to be important for the diet of several native bee species, changed because of nitrogen (N) addition. Not only did the overall amino acid content increase with N addition, but its profile was also affected, with the proportion of some amino acids increasing (e.g. isoleucine, leucine, serine, threonine), while decreasing for others (e.g. cysteine). These amino acids can have important effects on larval development and flower visitor behaviour. Further studies evaluating the effects on a diverse set of plant species and the consequent impacts on flower visitation and bee fitness are essential to better understand the full consequences of increased nitrogen availability in nutrient-limited ecosystems such as Cerrado.
