Exotic earthworms maintain soil biodiversity by altering bottom-up effects of plants on the composition of soil microbial groups and nematode communities

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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Soil microbial diversity–biomass relationships are driven by soil carbon content across global biomes

The ISME Journal ◽

10.1038/s41396-021-00906-0 ◽

2021 ◽

Author(s):

Felipe Bastida ◽

David J. Eldridge ◽

Carlos García ◽

G. Kenny Png ◽

Richard D. Bardgett ◽

...

Keyword(s):

Microbial Diversity ◽

Soil Carbon ◽

Soil Microbial Communities ◽

Ecosystem Functions ◽

Arid Environments ◽

Soil Microbial Diversity ◽

Soil Biodiversity ◽

Soil C ◽

Soil Microbial ◽

Biomass Ratio

AbstractThe relationship between biodiversity and biomass has been a long standing debate in ecology. Soil biodiversity and biomass are essential drivers of ecosystem functions. However, unlike plant communities, little is known about how the diversity and biomass of soil microbial communities are interlinked across globally distributed biomes, and how variations in this relationship influence ecosystem function. To fill this knowledge gap, we conducted a field survey across global biomes, with contrasting vegetation and climate types. We show that soil carbon (C) content is associated to the microbial diversity–biomass relationship and ratio in soils across global biomes. This ratio provides an integrative index to identify those locations on Earth wherein diversity is much higher compared with biomass and vice versa. The soil microbial diversity-to-biomass ratio peaks in arid environments with low C content, and is very low in C-rich cold environments. Our study further advances that the reductions in soil C content associated with land use intensification and climate change could cause dramatic shifts in the microbial diversity-biomass ratio, with potential consequences for broad soil processes.

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Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

Microorganisms ◽

10.3390/microorganisms9020211 ◽

2021 ◽

Vol 9 (2) ◽

pp. 211

Author(s):

Jie Gao ◽

Miao Liu ◽

Sixue Shi ◽

Ying Liu ◽

Yu Duan ◽

...

Keyword(s):

Microbial Community ◽

High Throughput Sequencing ◽

Carbon Fixation ◽

Microbial Community Composition ◽

Ecosystem Functions ◽

Microbial Composition ◽

Wetland Ecosystems ◽

Soil Microbial ◽

Geochemical Properties ◽

Microbial Groups

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

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Responses of soil microbial and nematode communities to aluminum toxicity in vegetated oil-shale-waste lands

Ecotoxicology ◽

10.1007/s10646-012-0966-4 ◽

2012 ◽

Vol 21 (8) ◽

pp. 2132-2142 ◽

Cited By ~ 4

Author(s):

Yuanhu Shao ◽

Weixin Zhang ◽

Zhanfeng Liu ◽

Yuxin Sun ◽

Dima Chen ◽

...

Keyword(s):

Oil Shale ◽

Aluminum Toxicity ◽

Nematode Communities ◽

Soil Microbial

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The influence of light on soil community structure and consequences for soil CO2, CO18O and COS exchange

10.5194/egusphere-egu2020-20422 ◽

2020 ◽

Author(s):

Lisa Wingate ◽

Clement Foucault ◽

Nicolas Fanin ◽

Joana Sauze ◽

Pierre-Alain Maron ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Soil Ph ◽

Isotope Composition ◽

Light Availability ◽

Alkaline Soils ◽

Soil Microbial ◽

Microbial Groups ◽

Taxonomic Groups ◽

Carbonyl Sulphide

The stable oxygen isotope composition of atmospheric CO2 and the mixing ratio of carbonyl sulphide (COS) are potential tracers of biospheric CO2 fluxes at large scales. However, the use of these tracers hinges on our ability to understand and better predict the activity of the enzyme carbonic anhydrase (CA) in different soil microbial groups, including phototrophs. Because different classes of the CA family (&#945;, &#946; and &#947;) may have different affinities to CO2 and COS and their expression should also vary between different microbial groups, differences in the community structure could impact the &#8216;community-integrated&#8217; CA activity differently for CO2 and COS. Four soils of different pH were incubated in the dark or with a diurnal cycle for forty days to vary the abundance of native phototrophs. Fluxes of CO2, CO18O and COS were measured to estimate CA activity alongside the abundance of bacteria, fungi and phototroph genes. The abundance of soil phototrophs increased most at higher soil pH. In the light, the strength of the soil CO2 sink and the CA-driven CO2-H2O isotopic exchange rates correlated with phototroph abundance. COS uptake rates were attributed to fungi whose abundance was positively enhanced in alkaline soils but only in the presence of increased phototrophs. In addition we developed a metabarcoding approach to reveal the interactions of specific taxonomic groups incuding photosynthetic eukaryotic algae and cyanobacteria when exposed to light and their impact on flux rates. Our findings demonstrate that soil-atmosphere CO2, COS and CO18O fluxes are strongly regulated by the microbial community structure in response to changes in soil pH and light availability and support the idea that different members of the microbial community express different classes of CA, with different affinities to CO2 and COS.

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Soil Microbial Activity and Diversity in Response to Soil Chemical Factors in Agricultural Soils

Journal of Tropical Soils ◽

10.5400/jts.2019.v24i1.43-51 ◽

2019 ◽

Vol 24 (1) ◽

pp. 43

Author(s):

Lily Ishak ◽

Philip Hugh Brown

Keyword(s):

Microbial Communities ◽

Agricultural Soils ◽

Soil Health ◽

Soil Microbial Communities ◽

Soil Microbial Activity ◽

Soil Microbial Diversity ◽

Soil Microbial ◽

Microbial Responses ◽

Chemical Factors ◽

Microbial Groups

The role of microbial communities in maintaining soil health is mostly influenced by chemical condition of soil. Microbial communities vary in response to soil chemical factors. The contradictive results from previous findings emphasise that it is difficult to define a pattern of the influence of soil chemical factors on soil microbial diversity and activity. The aim of the study was to assess soil microbial responses to soil chemical factors in agricultural soils. Composite soil (Dermosol order) samples taken from 16 commercial crop sites in Bundaberg, Queensland, Australia, were chemically and biologically analysed. It was found that bacterial and fungal activity and diversity were significantly affected by soil EC, SOM and NO3-N content, but were not influenced by soil pH, CEC, and Ca:Mg ratio. The diversity of bacterial and fungal communities displayed a positive linear relationship with soil EC, whereas the activity and diversity of these two microbial groups and SOM displayed a significant quadratic relationship. The finding suggested that microbial community was predominantly influenced by SOM content.

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

10.1101/623264 ◽

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.

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Responses of Soil Microbial Communities to Robinia Pseudoacacia Plantations of Different Ages in A Loess Area

10.20944/preprints201709.0016.v1 ◽

2017 ◽

Cited By ~ 1

Author(s):

Bingxue Zhang ◽

Rumeng Zhao ◽

Boyuan Bi ◽

Fengpeng Han

Keyword(s):

Soil Depth ◽

Robinia Pseudoacacia ◽

Principal Component ◽

Stand Age ◽

Soil Layers ◽

Loess Area ◽

Soil Microbial ◽

Different Ages ◽

Microbial Groups ◽

The Individual

Phospholipid fatty acids (PLFAs) can be used as biomarkers for qualitative and quantitative analyses of soil microbial community diversity. In this study, we collected soil samples at 10-cm intervals to a depth of 1 m from Robinia pseudoacacia plantations of four different ages (10, 15, 25 and 40 years) in a loess area and analysed the soil microbial community structure by PLFA analysis. A total of 97 PLFAs were detected in soils of R. pseudoacacia plantations of different ages. The individual PLFA contents gradually decreased in the 0- to 40-cm soil layers, with little variation in the 40- to 100-cm soil layers. The individual PLFAs were similarly distributed in the soils of R. pseudoacacia plantations of different ages, and there was a clear variation with stand age and soil depth. The individual PLFA contents in the 0- to 20-cm soil layers were highest for the 25-year-old plantation, while those in the 20- to 40-cm soil layers were relatively high for the 25- and 40-year-old plantations; the 16:0 content was the highest among individual PLFAs. The total PLFA content and the PLFA contents of different microbial groups [bacteria, fungi, Gram-positive bacteria (G+), Gram-negative bacteria (G-) and actinomycetes] initially increased before decreasing in the soils of R. pseudoacacia plantations with increasing stand age, whereas these contents gradually decreased with increasing soil depth; the highest PLFA contents was found in the 25-year-old plantation. The total PLFA content and the contents of fungal, G- and actinomycete PLFAs in the soils of R. pseudoacacia plantations differed significantly among stands of different ages in the 0- to 10-cm, 10- to 20-cm and 30- to 40-cm soil layers, while no significant differences were found in the 20- to 30-cm soil layers; the G+ and bacterial PLFAs contents in each of the 0- to 40-cm soil layers were significantly different. The PLFA ratios between different microbial groups differed among the stands of different ages. The fungi/bacteria ratio showed a “decrease-increase-decrease” trend with stand age, while the G+/G- ratio showed an “increase-decrease” trend. The saturated/monounsaturated PLFA ratio initially decreased before plateauing, while the opposite trend was observed for the cyclopropyl/precursor ratio. The PLFA contents of different microbial groups were ranked as follows: bacteria > G- > G+ > actinomycetes > fungi. In the principle component analysis, 18:1ω9c, 10Me18:0, i17:0, a17:0, 18:1ω7c, 18:1ω5c and 18:0 made the greatest contribution to principal component 1, and a14:0, i14:0 3OH, i14:0, i14:1ω7c and 14:0 made the greatest contribution to principal component 2. In conclusion, soil nutrient status and other soil eco-environmental stress factors should be considered in 10- to 25-year-old (particularly ~15-year-old) plots for the management of R. pseudoacacia plantations to prevent forest soil degradation and improve forest stand quality, thereby achieving better soil and water conservation and environmental improvement in R. pseudoacacia plantations.

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Allocation and turnover of rhizodeposited carbon in different soil microbial groups

Soil Biology and Biochemistry ◽

10.1016/j.soilbio.2020.107973 ◽

2020 ◽

Vol 150 ◽

pp. 107973 ◽

Cited By ~ 1

Author(s):

Junsheng Huang ◽

Weixing Liu ◽

Meifeng Deng ◽

Xin Wang ◽

Zhenhua Wang ◽

...

Keyword(s):

Soil Microbial ◽

Microbial Groups

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Impact of Agrochemicals on Soil Microbiota and Management: A Review

Land ◽

10.3390/land9020034 ◽

2020 ◽

Vol 9 (2) ◽

pp. 34 ◽

Cited By ~ 66

Author(s):

Ram Meena ◽

Sandeep Kumar ◽

Rahul Datta ◽

Rattan Lal ◽

Vinod Vijayakumar ◽

...

Keyword(s):

Smallholder Farmers ◽

Disease Incidence ◽

Animal Health ◽

Crop Protection ◽

World Health ◽

Soil Microbial Diversity ◽

Soil Biodiversity ◽

Nutritional Security ◽

Soil Microbial ◽

The Impact

The World Health Organization (WHO) states that in developing nations, there are three million cases of agrochemical poisoning. The prolonged intensive and indiscriminate use of agrochemicals adversely affected the soil biodiversity, agricultural sustainability, and food safety, bringing in long-term harmful effects on nutritional security, human and animal health. Most of the agrochemicals negatively affect soil microbial functions and biochemical processes. The alteration in diversity and composition of the beneficial microbial community can be unfavorable to plant growth and development either by reducing nutrient availability or by increasing disease incidence. Currently, there is a need for qualitative, innovative, and demand-driven research in soil science, especially in developing countries for facilitating of high-quality eco-friendly research by creating a conducive and trustworthy work atmosphere, thereby rewarding productivity and merits. Hence, we reviewed (1) the impact of various agrochemicals on the soil microbial diversity and environment; (2) the importance of smallholder farmers for sustainable crop protection and enhancement solutions, and (3) management strategies that serve the scientific community, policymakers, and land managers in integrating soil enhancement and sustainability practices in smallholder farming households. The current review provides an improved understanding of agricultural soil management for food and nutritional security.

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