scholarly journals History Leaves Its Mark on Soil Bacterial Diversity

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Jennifer B. H. Martiny
Keyword(s):  
Climate Change ◽  
Microbial Diversity ◽  
Bacterial Diversity ◽  
Soil Bacteria ◽  
Future Climate Change ◽  
Soil Bacterial Diversity ◽  
Soil Microbial Diversity ◽  
Climate Conditions ◽  
Soil Microbial ◽  
Evolutionary Diversification

ABSTRACT Dispersal is closely tied to the origin and maintenance of microbial diversity. With its focus on a narrow group of soil bacteria, recent work by Andam and colleagues on Streptomyces has provided perhaps the strongest support so far that some bacterial diversity in soils can be attributed to regional endemism (C. P. Andam et al., mBio 7:e02200-15, 2016, http://dx.doi.org/10.1128/mBio.02200-15 ). This means that dispersal is limited enough to allow for evolutionary diversification. Further analyses suggest that signatures of climate conditions more than 10,000 years ago can be detected in contemporary populations of this genus. These legacies have implications for how future climate change might alter soil microbial diversity.

scholarly journals Contrasting Biogeographic Patterns of Bacterial and Archaeal Diversity in the Top- and Subsoils of Temperate Grasslands

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Nana Liu ◽  
Huifeng Hu ◽  
Wenhong Ma ◽  
Ye Deng ◽  
Yuqing Liu ◽  
...  
Keyword(s):  
Climate Change ◽  
Microbial Diversity ◽  
Bacterial Diversity ◽  
Archaeal Diversity ◽  
Soil Microbial Diversity ◽  
Temperate Grasslands ◽  
Diversity Patterns ◽  
Biogeographic Patterns ◽  
Soil Microbial ◽  
Contemporary Climate

ABSTRACT Biogeographic patterns and drivers of soil microbial diversity have been extensively studied in the past few decades. However, most research has focused on the topsoil, while the subsoil is assumed to have microbial diversity patterns similar to those of the topsoil. Here we compared patterns and drivers of microbial alpha and beta diversity in and between topsoils (0 to 10 cm) and subsoils (30 to 50 cm) of temperate grasslands in Inner Mongolia of China, covering an ∼1,500-km transect along an aridity gradient. Counter to the conventional assumption, we find contrasting biogeographic patterns of diversity and influencing factors for different bacterial and archaeal groups and between depths. While bacterial diversity remains constant or increases with increasing aridity in topsoil and decreases in subsoil, archaeal diversity decreases in topsoil and remains constant in subsoil. Microbial diversity in the topsoil is most strongly influenced by aboveground vegetation and contemporary climate but is most strongly influenced by the factor historical temperature anomaly since the Last Glacial Maximum (LGM) and by soil pH in the subsoil. Moreover, the biogeographic patterns of topsoil-subsoil community dissimilarities vary for different microbial groups and are overall most strongly influenced by soil fertility differences between depths for bacteria and by contemporary climate for archaea. These findings suggest that diversity patterns observed in the topsoil may not be readily applied to the subsoil horizons. For the subsoil in particular, historical climate plays a vital role in the spatial variation of bacterial diversity. Overall, our study provides novel information for understanding and predicting soil microbial diversity patterns at depth. IMPORTANCE Exploring the biogeographic patterns of soil microbial diversity is critical for understanding mechanisms underlying the response of soil processes to climate change. Using top- and subsoils from an ∼1,500-km temperate grassland transect, we find divergent patterns of microbial diversity and its determinants in the topsoil versus the subsoil. Furthermore, we find important and direct legacy effects of historical climate change on the microbial diversity of subsoil yet indirect effects on topsoil. Our findings challenge the conventional assumption of similar geographic patterns of soil microbial diversity along soil profiles and help to improve our understanding of how soil microbial communities may respond to future climate change in different regions with various climate histories.

scholarly journals TRFLP Analysis of the Effect of a Forest-to-Gap Ectone on Soil Microbial Diversity

2014 ◽  
Author(s):  
Ronald Smith
Keyword(s):  
Microbial Diversity ◽  
Bacterial Diversity ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Restriction Enzyme Digestion ◽  
Dna Fragments ◽  
Soil Bacterial Diversity ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Soil Bacterial

<p>To investigate how soil microbial diversity is influenced by the formation of an experimental edge-creating gap within a southern New England oak-hickory forest, I used a molecular fingerprinting technique known as terminal restriction fragment length polymorphism (TRFLP). Sequence variability in the 16S ribosomal RNA (rRNA) gene in soil bacterial communities is detected by differences in the length and abundance of fragments produced by digesting PCR products amplified from rRNA genes. The different patterns observed are assumed to represent unique phylotypes.</p> <p>How does the forest-gap ecotone influence soil bacterial diversity? Based on other studies, I hypothesized that the edge would contain the most diverse bacterial community, followed by the gap, and as distance from the gap into the forest increased, bacterial diversity would decrease.</p> <p>Soil samples were collected along 40m transects perpendicular to the northern edge of the gap. DNA was extracted from each sample, PCR was used to amplify the 16S rRNA gene, and DNA fragments were cut by restriction enzyme digestion and separated via electrophoresis. The DNA fragments were analyzed by TRFLP.</p> <p>Environmental variables (soil pH, soil temperature and soil gravimetric moisture) were different in the gap compared to all other distances, but not significantly so. Phylotype richness and diversity (Simpson’s index) was greatest at the edge. Canonical Correspondence Analysis (CCA) produced a phylotype-by-distance ordination that supports my hypothesis and shows that the edge is an ecotone (transitional zone) between the gap and forest.</p>

scholarly journals Agricultural practice negatively affects soil microbial diversity and nitrogen functional genes comparing to adjacent native forest soils

2021 ◽  
Author(s):  
Tiehang Wu ◽  
Michael Sabula ◽  
Holli Milner ◽  
Gary Strickland ◽  
Gan Liu
Keyword(s):  
Community Structure ◽  
Bacterial Diversity ◽  
Forest Soils ◽  
Agricultural Practices ◽  
Functional Genes ◽  
Agricultural Practice ◽  
Soil Bacterial Diversity ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Soil Bacterial

Soil microbial diversity and community are determined by anthropogenic activities and environmental conditions, which greatly affect the functioning of ecosystem. We investigated the soil bacterial diversity, communities, and nitrogen (N) functional genes with different disturbance intensity levels from crop, transition, to forest soils at three locations in the coastal region of Georgia, USA. Illumina high-throughput DNA sequencing based on bacterial 16S rRNA genes were performed for bacterial diversity and community analyses. Nitrifying (AOB amoA) and denitrifying (nirK) functional genes were further detected using quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE). Soil bacterial community structure determined by Illumina sequences were significantly different between crop and forest soils (p < 0.01), as well as between crop and transition soils (p = 0.01). However, there is no difference between transition and forest soils. Compared to less disturbed forest, agricultural practice significantly decreased soil bacterial richness and Shannon diversity. Soil pH and nitrate contents together contributed highest for the observed different bacterial communities (Correlations = 0.381). Two OTUs (OTU5, OTU8) belonging to Acidobacteriales species decreased in crop soils, however, agricultural practices significantly increased an OTU (OTU4) of Nitrobacteraceae. The relative abundance of AOB amoA gene was significantly higher in crop soils than in forest and transition soils. Distinct grouping of soil denitrifying bacterial nirK communities was observed and agricultural practices significantly decreased the diversity of nirK gene compared to forest soils. Anthropogenic effects through agricultural practices negatively affecting the soil bacterial diversity, community structure, and N functional genes.

scholarly journals Plant Taxonomic Diversity Better Explains Soil Fungal and Bacterial Diversity than Functional Diversity in Restored Forest Ecosystems

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 479 ◽  
Author(s):  
Hanif ◽  
Guo ◽  
Moniruzzaman ◽  
He ◽  
Yu ◽  
...  
Keyword(s):  
Species Richness ◽  
Microbial Diversity ◽  
Soil Properties ◽  
Bacterial Diversity ◽  
Functional Diversity ◽  
Forest Ecosystems ◽  
Taxonomic Diversity ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Bacterial Richness

Plant attributes have direct and indirect effects on soil microbes via plant inputs and plant-mediated soil changes. However, whether plant taxonomic and functional diversities can explain the soil microbial diversity of restored forest ecosystems remains elusive. Here, we tested the linkage between plant attributes and soil microbial communities in four restored forests (Acacia species, Eucalyptus species, mixed coniferous species, mixed native species). The trait-based approaches were applied for plant properties and high-throughput Illumina sequencing was applied for fungal and bacterial diversity. The total number of soil microbial operational taxonomic units (OTUs) varied among the four forests. The highest richness of fungal OTUs was found in the Acacia forest. However, bacterial OTUs were highest in the Eucalyptus forest. Species richness was positively and significantly related to fungal and bacterial richness. Plant taxonomic diversity (species richness and species diversity) explained more of the soil microbial diversity than the functional diversity and soil properties. Prediction of fungal richness was better than that of bacterial richness. In addition, root traits explained more variation than the leaf traits. Overall, plant taxonomic diversity played a more important role than plant functional diversity and soil properties in shaping the soil microbial diversity of the four forests.

scholarly journals Contrasting biogeographic patterns of bacterial and archaeal diversity in the top- and subsoils of temperate grasslands

2019 ◽  
Author(s):  
Nana Liu ◽  
Huifeng Hu ◽  
Wenhong Ma ◽  
Ye Deng ◽  
Yuqing Liu ◽  
...  
Keyword(s):  
Climate Change ◽  
Microbial Diversity ◽  
Temperature Anomaly ◽  
Soil Microbial Diversity ◽  
Temperate Grasslands ◽  
Diversity Patterns ◽  
Biogeographic Patterns ◽  
Soil Microbial ◽  
Historical Temperature ◽  
Microbial Groups

ABSTRACTBiogeographic patterns and drivers of soil microbial diversity have been extensively studied in the past few decades. However, most research has focused on the topsoil while the subsoil is assumed to have similar microbial diversity patterns as the topsoil. Here we compare patterns and drivers of microbial diversity in the top- (0-10 cm) versus subsoils (30-50 cm) of temperate grasslands in Inner Mongolia of China along an aridity gradient covering a ~1500-km transect from arid to mesic ecosystems. Counter to the conventional assumption, we find contrasting biogeographic patterns of diversity and influencing factors for different bacterial and archaeal groups and between depths. While bacterial diversity increases with increasing aridity, archaeal diversity decreases. Microbial diversity in the topsoil is most strongly influenced by aboveground vegetation, but is most strongly influenced by historical temperature anomaly since the Last Glacial Maximum (LGM) in the subsoil. Moreover, the biogeographic patterns of top-subsoil diversity difference varies for different microbial groups and is overall most strongly influenced by soil fertility difference between depths and historical temperature anomaly. These findings suggest that diversity patterns observed in the topsoil may not be readily applied to the subsoil horizons. For the subsoil in particular, historical climate plays a vital role in the distribution of various microbial groups. Overall, our study provides novel information for understanding and predicting soil microbial diversity patterns at depth.IMPORTANCEExploring the biogeographic patterns of soil microbial diversity is critical for understanding mechanisms underlying the response of soil processes to climate change. Using top- and subsoils from a ~1500-km temperature grassland transect, we find divergent patterns of microbial diversity and its determinants in the top-versus subsoils. Furthermore, we find important legacy effect of historical climate change on the microbial diversity of subsoil but not topsoil. Our findings challenge the conventional assumption of similar geographic patterns of soil microbial diversity along soil profiles and help to improve our understanding of how soil microbial communities may respond to future climate change in different regions with varied climate history.

scholarly journals Agricultural practice altering soil microbial diversity and nitrogen functional genes comparing to adjacent native forest soils

2021 ◽  
Author(s):  
Tiehang Wu ◽  
Michael Sabula ◽  
Holli Milner ◽  
Gary Strickland ◽  
Gan Liu
Keyword(s):  
Community Structure ◽  
Bacterial Diversity ◽  
Forest Soils ◽  
Agricultural Practices ◽  
Functional Genes ◽  
Agricultural Practice ◽  
Soil Bacterial Diversity ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Soil Bacterial

Soil microbial diversity and community are determined by anthropogenic activities and environmental conditions, which greatly affect the functioning of ecosystem. We investigated the soil bacterial diversity, communities, and nitrogen (N) functional genes with different disturbance intensity levels from crop, transition, to forest soils at three locations in the coastal region of Georgia, USA. Illumina high-throughput DNA sequencing based on bacterial 16S rRNA genes were performed for bacterial diversity and community analyses. Nitrifying (AOB amoA) and denitrifying (nirK) functional genes were further detected using quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE). Soil bacterial community structure determined by Illumina sequences were significantly different between crop and forest soils (p < 0.01), as well as between crop and transition soils (p = 0.01). However, there is no difference between transition and forest soils. Compared to less disturbed forest, agricultural practice significantly decreased soil bacterial richness and Shannon diversity. Soil pH and nitrate contents together contributed highest for the observed different bacterial communities (Correlations = 0.381). Two OTUs (OTU5, OTU8) belonging to Acidobacteriales species decreased in crop soils, however, agricultural practices significantly increased an OTU (OTU4) of Nitrobacteraceae. The relative abundance of AOB amoA gene was significantly higher in crop soils than in forest and transition soils. Distinct grouping of soil denitrifying bacterial nirK communities was observed and agricultural practices significantly decreased the diversity of nirK gene compared to forest soils. Anthropogenic effects through agricultural practices negatively affecting the soil bacterial diversity, community structure, and N functional genes.

scholarly journals Increasing aridity reduces soil microbial diversity and abundance in global drylands

2015 ◽  
Vol 112 (51) ◽  
pp. 15684-15689 ◽  
Author(s):  
Fernando T. Maestre ◽  
Manuel Delgado-Baquerizo ◽  
Thomas C. Jeffries ◽  
David J. Eldridge ◽  
Victoria Ochoa ◽  
...  
Keyword(s):  
Climate Change ◽  
Soil Bacteria ◽  
Soil Microbial Communities ◽  
Terrestrial Ecosystems ◽  
Soil Microbial Diversity ◽  
Change Models ◽  
Soil Microbial ◽  
Soil Bacteria And Fungi ◽  
Abundance And Diversity ◽  
Bacteria And Fungi

Soil bacteria and fungi play key roles in the functioning of terrestrial ecosystems, yet our understanding of their responses to climate change lags significantly behind that of other organisms. This gap in our understanding is particularly true for drylands, which occupy ∼41% of Earth´s surface, because no global, systematic assessments of the joint diversity of soil bacteria and fungi have been conducted in these environments to date. Here we present results from a study conducted across 80 dryland sites from all continents, except Antarctica, to assess how changes in aridity affect the composition, abundance, and diversity of soil bacteria and fungi. The diversity and abundance of soil bacteria and fungi was reduced as aridity increased. These results were largely driven by the negative impacts of aridity on soil organic carbon content, which positively affected the abundance and diversity of both bacteria and fungi. Aridity promoted shifts in the composition of soil bacteria, with increases in the relative abundance of Chloroflexi and α-Proteobacteria and decreases in Acidobacteria and Verrucomicrobia. Contrary to what has been reported by previous continental and global-scale studies, soil pH was not a major driver of bacterial diversity, and fungal communities were dominated by Ascomycota. Our results fill a critical gap in our understanding of soil microbial communities in terrestrial ecosystems. They suggest that changes in aridity, such as those predicted by climate-change models, may reduce microbial abundance and diversity, a response that will likely impact the provision of key ecosystem services by global drylands.

scholarly journals Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes

2016 ◽  
Author(s):  
Andrew T. Nottingham ◽  
Noah Fierer ◽  
Benjamin L. Turner ◽  
Jeanette Whitaker ◽  
Nick J. Ostle ◽  
...  
Keyword(s):  
Species Richness ◽  
Microbial Diversity ◽  
Tropical Forest ◽  
Soil Ph ◽  
Soil Bacteria ◽  
Environmental Drivers ◽  
Future Climate Change ◽  
Soil Microbial Diversity ◽  
Tropical Mountains ◽  
Bacteria And Fungi

SummaryMore than 200 years ago, von Humboldt reported decreases in tropical plant species richness with increasing elevation and decreasing temperature. Surprisingly, co-ordinated patterns in plant, bacterial and fungal diversity on tropical mountains are yet to be observed, despite the central role of soil microorganisms in terrestrial biogeochemistry. We studied an Andean transect traversing 3.5 km in elevation to test whether the species diversity and composition of tropical forest plants, soil bacteria and fungi can follow similar biogeographical patterns with shared environmental drivers. We found co-ordinated changes with elevation in all three groups: species richness declined as elevation increased, and the compositional-dissimilarity of communities increased with increased separation in elevation, although changes in plant diversity were larger than in bacteria and fungi. Temperature was the dominant driver of these diversity gradients, with weak influences of edaphic properties, including soil pH. The gradients in microbial diversity were strongly correlated with the activities of enzymes involved in organic matter cycling, and were accompanied by a transition in microbial traits towards slower-growing, oligotrophic taxa at higher elevations. We provide the first evidence of co-ordinated temperature-driven patterns in the diversity and distribution of three major biotic groups in tropical ecosystems: soil bacteria, fungi and plants. These findings suggest that, across landscape scales of relatively constant soil pH, inter-related patterns of plant and microbial communities with shared environmental drivers can occur, with large implications for tropical forest communities under future climate change.

scholarly journals Soil Bacterial Diversity and Productivity of Coffee - Shade Tree Agro-ecosystems

2012 ◽  
Vol 17 (2) ◽  
pp. 181 ◽  
Author(s):  
Rusdi Evizal ◽  
. Tohari ◽  
Irfan Dwidja Prijambada ◽  
Jaka Widada ◽  
Donny Widianto
Keyword(s):  
Bacterial Diversity ◽  
Soil Bacteria ◽  
Coffee Bean ◽  
Soil Bacterial Diversity ◽  
Soil Microbial Diversity ◽  
Organic C ◽  
Shade Coffee ◽  
Bean Yield ◽  
Soil Bacterial ◽  
Positive Effect

Coffee productions should have environmental value such as providing high soil microbial diversity while producing high yield. To examine that purposes, two experimental plots were constucted at benchmark site of Conservation and Sustainable Management of Below-Ground Biodiversity (CSM-BGBD), in Sumberjaya Subdistrict, West Lampung, Indonesia, during 2007-2010. Types of coffee agro-ecosystem to be examined were Coffea canephora with shade trees of Gliricidia sepium, Erythrina sububrams, Michelia champaca, and no shade. Two plots were constructed at 5-years-coffee and 15-years-coffee. Diversity of soil bacteria was determined based on DNA finger printing of total soil bacteria using Ribosomal Intergenic Spacer Analysis (RISA) method. The results showed that: (1) For mature coffee (15 years old), shade-grown coffee agro-ecosystems had higher soil bacterial diversity than those of no shade coffee agro-ecosystem, (2) Shaded coffee agro-ecosystems were able to conserve soil bacterial diversity better than no-shade coffee agro-ecosystem. Soil organic C and total litter biomass had positive effect on soil bacterial diversity, (3) Types of agro-ecosystem significantly affect the bean yield of 15 years coffee. Coffee agro-ecosystems shaded by legume trees had higher yield than those of non-legume shade and no shade coffee agro-ecosystem, (4) Shannon-Weaver indices of soil bacterial diversity together with weed biomass and N content of coffee leaf had positive effect on coffee bean yield.

scholarly journals Soil microbial inoculation during flood events shapes headwater stream microbial communities and diversity

2021 ◽  
Author(s):  
Florian Caillon ◽  
Katharina Besemer ◽  
Peter Peduzzi ◽  
Jakob Schelker
Keyword(s):  
Microbial Diversity ◽  
Bacterial Diversity ◽  
Soil Water ◽  
Headwater Streams ◽  
High Flow ◽  
Low Flow ◽  
Flood Events ◽  
Flow Conditions ◽  
Soil Microbial ◽  
Microbial Inoculation

AbstractFlood events are now recognized as potentially important occasions for the transfer of soil microbes to stream ecosystems. Yet, little is known about these “dynamic pulses of microbial life” for stream bacterial community composition (BCC) and diversity. In this study, we explored the potential alteration of stream BCC by soil inoculation during high flow events in six pre-alpine first order streams and the larger Oberer Seebach. During 1 year, we compared variations of BCC in soil water, stream water and in benthic biofilms at different flow conditions (low to intermediate flows versus high flow). Bacterial diversity was lowest in biofilms, followed by soils and highest in headwater streams and the Oberer Seebach. In headwater streams, bacterial diversity was significantly higher during high flow, as compared to low flow (Shannon diversity: 7.6 versus 7.9 at low versus high flow, respectively, p < 0.001). Approximately 70% of the bacterial operational taxonomic units (OTUs) from streams and stream biofilms were the same as in soil water, while in the latter one third of the OTUs were specific to high flow conditions. These soil high-flow OTUs were also found in streams and biofilms at other times of the year. These results demonstrate the relevance of floods in generating short and reoccurring inoculation events for flowing waters. Moreover, they show that soil microbial inoculation during high flow enhances microbial diversity and shapes fluvial BCC even during low flow. Hence, soil microbial inoculation during floods could act as a previously overlooked driver of microbial diversity in headwater streams.

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