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 A meta-analysis of the effect of organic and mineral fertilizers on soil microbial diversity

2020 ◽  
Author(s):  
Daniel P. Bebber ◽  
Victoria R. Richards
Keyword(s):  
Microbial Biomass ◽  
Microbial Diversity ◽  
Meta Analysis ◽  
Taxonomic Diversity ◽  
Mineral Fertilizers ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Meta Analyses ◽  
Fertilizer Regimes ◽  
Diversity Metrics

ABSTRACTThe Green Revolution of agriculture was in part driven by application of synthetic mineral fertilizers, largely supplanting organic manure as a source of the major nutrients nitrogen, phosphorous and potassium (NPK). Though enhancing crop production and global food security, fertilizers have contributed to soil acidification, eutrophication of water bodies, and greenhouse gas emissions. Organic agriculture, employing manures or composts, has been proposed as a way of mitigating these undesirable effects. Of particular interest is the effect of fertilizer regime on soil microbes, which are key to nutrient cycling, plant health and soil structure. Meta-analyses of experimental studies indicate that mineral fertilizer increases soil microbial biomass over unfertilized controls, and that organic fertilizers increase microbial biomass and activity over mineral fertilizers. However, the effect of fertilizers on soil microbial diversity remains poorly understood. Since biological diversity is an important determinant of ecosystem function and a fundamental metric in community ecology, the effects of fertilizer regimes on soil microbial diversity are of theoretical and applied interest. Here, we conduct a meta-analysis of 31 studies reporting microbial diversity metrics in mineral fertilized (NPK), organically fertilized (ORG) and unfertilized control (CON) soils. Of these studies, 26 reported taxonomic diversity derived from sequencing, gradient gel electrophoresis, RFLP, or dilution plate assay. Functional diversity, derived from Biolog Ecoplate™ measures of carbon substrate metabolism, was reported in 8 studies, with 3 studies reporting both diversity metrics. We found that functional diversity was on average 2.6 % greater in NPK compared with CON, 6.8 % greater in ORG vs CON and 3.6 % greater in ORG vs NPK. Prokaryote taxonomic diversity was not significantly different between NPK and CON, 4.2 % greater in ORG vs CON and 4.6 % greater in ORG vs. NPK. Fungal taxonomic diversity was not significantly different between NPK or ORG vs CON, but 5.4 % lower between ORG and NPK. There was very high residual heterogeneity in all meta-analyses of soil diversity, suggesting that a large amount of further research with detailed analysis of soil properties is required to fully understand the influence of fertilizer regimes on microbial diversity and ecosystem function.

scholarly journals Soil microbial diversity in organic and non-organic pasture systems

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11184
Author(s):  
Mohan Acharya ◽  
Amanda J. Ashworth ◽  
Yichao Yang ◽  
Joan M. Burke ◽  
Jung Ae Lee ◽  
...  
Keyword(s):  
Species Richness ◽  
Microbial Diversity ◽  
Bacterial Species ◽  
Soil Microbiome ◽  
Organic Soils ◽  
Pasture Management ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Organic Systems ◽  
Microbiome Diversity

Understanding the effects of organic pasture management on the soil microbiome is important for sustainable forage production since soil microbiome diversity contributes to improved nutrient cycling, soil structure, plant growth, and environmental resiliency; however, the soil microbiome response to pasture management is largely unknown. This study assessed the soil microbial diversity, richness, and community structure following 10 years of pasture management (organic or non-organic) of the V4 region of the 16S rRNA using the Illumina MiSeq platform. Soil samples were collected from 0–15 cm in July and August from 2017–2018 and soil nutrient properties (nutrients, carbon, nitrogen, and pH) quantified and correlated with soil microbial diversity. Overall, greater soil bacterial species richness (P ≤ 0.05) occurred in organic relative to non-organic (conventional) systems. Management affected bacterial species richness (Chao1), with greater richness occurring in organic pasture soils and less richness occurring in non-organic systems (P ≤ 0.05). Similarly, management affected bacterial evenness (Simpson’s index), with a more diverse community occurring in organically managed soils relative to non-organic pastures (P ≤ 0.05). Linear discriminant analysis effect size analysis showed statistically significant and biologically consistent differences in bacterial taxa in organic compared with non-organic soils. Therefore, there was a shift in bacterial community structure in organic relative to non-organic soils (P ≤ 0.05). Additionally, soil nutrients (Fe, Mg, Ni, S, Al, K, Cd, and Cu), pH, C, and N were correlated with one or more dominant bacterial phyla (Gemmatimonadetes, Planctomycetes, Firmicutes, Chloroflexi, Actinobacteria, and Acidobacteria). Overall, pasture management affected soil microbial diversity, with greater diversity occurring in organic than non-organic systems, likely owing to applications of organic poultry litter in organic systems compared to non-organic management (use of inorganic-fertilizers and herbicides). Results indicate that when pastures are converted to organic production systems, soil microbial richness and diversity may increase, thereby resulting in enhanced soil microbiome diversity and overall ecosystem services.

scholarly journals Linkage between tree species richness and soil microbial diversity improves phosphorus bioavailability

2019 ◽  
Vol 33 (8) ◽  
pp. 1549-1560 ◽  
Author(s):  
Huili Wu ◽  
Wenhua Xiang ◽  
Shuai Ouyang ◽  
David I. Forrester ◽  
Bo Zhou ◽  
...  
Keyword(s):  
Species Richness ◽  
Microbial Diversity ◽  
Tree Species ◽  
Soil Microbial Diversity ◽  
Soil Microbial ◽  
Tree Species Richness

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 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 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 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.

scholarly journals Improvement of Soil Microbial Diversity through Sustainable Agricultural Practices and Its Evaluation by -Omics Approaches: A Perspective for the Environment, Food Quality and Human Safety

2021 ◽  
Vol 9 (7) ◽  
pp. 1400
Author(s):  
Marta Bertola ◽  
Andrea Ferrarini ◽  
Giovanna Visioli
Keyword(s):  
Microbial Diversity ◽  
Food Quality ◽  
Plant Biomass ◽  
Soil Microbial Communities ◽  
Well Being ◽  
Plant Health ◽  
Soil Microbiome ◽  
Soil Microbial Diversity ◽  
Soil Biodiversity ◽  
Soil Microbial

Soil is one of the key elements for supporting life on Earth. It delivers multiple ecosystem services, which are provided by soil processes and functions performed by soil biodiversity. In particular, soil microbiome is one of the fundamental components in the sustainment of plant biomass production and plant health. Both targeted and untargeted management of soil microbial communities appear to be promising in the sustainable improvement of food crop yield, its nutritional quality and safety. –Omics approaches, which allow the assessment of microbial phylogenetic diversity and functional information, have increasingly been used in recent years to study changes in soil microbial diversity caused by agronomic practices and environmental factors. The application of these high-throughput technologies to the study of soil microbial diversity, plant health and the quality of derived raw materials will help strengthen the link between soil well-being, food quality, food safety and human health.

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