Effect of Rainfall-Induced Soil Geochemistry Dynamics on Grassland Soil Microbial Communities

ABSTRACTIn Mediterranean-type grassland ecosystems, the timing of rainfall events controls biogeochemical cycles, as well as the phenology and productivity of plants and animals. Here, we investigate the effect of short-term (days) soil environmental conditions on microbial community structure and composition during a natural wetting and drying cycle. Soil samples were collected from a meadow in Northern California at four time points after the first two rainfall events of the rainy season. We used 16S rRNA microarrays (PhyloChip) to track changes in bacterial and archaeal community composition. Microbial communities at time points 1 and 3 were significantly different than communities at time points 2 and 4. Based on ordination analysis, the available carbon, soil moisture, and temperature explained most of the variation in community structure. For the first time, a complementary and more comprehensive approach using linear regression and generalized logical networks were used to identify linear and nonlinear associations among environmental variables and with the relative abundance of subfamilies. Changes in soil moisture and available carbon were correlated with the relative abundance of many phyla. Only the phylumActinobacteriashowed a lineage-specific relationship to soil moisture but not to carbon or nitrogen. The results indicate that the use of a high taxonomic rank in correlations with nutritional indicators might obscure divergent subfamily-level responses to environmental parameters. An important implication of this research is that there is short-term variation in microbial community composition driven in part by rainfall fluctuation that may not be evident in long-term studies with coarser time resolution.

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Microbial subnetworks related to short-term diel O2fluxes within geochemically distinct freshwater wetlands

10.1101/363226 ◽

2018 ◽

Author(s):

Dean J. Horton ◽

Matthew J. Cooper ◽

Anthony J. Wing ◽

Peter S. Kourtev ◽

Donald G. Uzarski ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Archaeal Community ◽

Freshwater Wetlands ◽

Freshwater Wetland ◽

Short Term ◽

Wetland Ecosystems ◽

Biogeochemical Transformations ◽

Physical And Chemical

ABSTRACTO2concentrations often fluctuate over diel timescales within wetlands, driven by temperature, sunlight, photosynthesis, and respiration. These daily fluxes have been shown to impact biogeochemical transformations (e.g. denitrification), which are mediated by the residing microbial community. However, little is known about how resident microbial communities respond to diel dramatic physical and chemical fluxes in freshwater wetland ecosystems. In this study, total microbial (bacterial and archaeal) community structure was significantly related to diel time points in just one out of four distinct freshwater wetlands sampled. This suggests that daily environmental shifts may influence wetlands differentially based upon the resident microbial community and specific physical and chemical conditions of a freshwater wetland. However, when exploring at finer resolutions of the microbial communities within each wetland, subcommunities within two wetlands were found to correspond to fluctuating O2levels. Microbial taxa that were found to be susceptible to fluctuating O2levels within these subnetworks may have intimate ties to metabolism and/or diel redox cycles. This study highlights that freshwater wetland microbial communities are often stable in community structure when confronted with short-term O2fluxes, however, specialist taxa may be sensitive to these same fluxes.

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Permafrost-derived dissolved organic matter character controls microbial community composition in Arctic coastal waters

10.5194/egusphere-egu21-13069 ◽

2021 ◽

Author(s):

Anders Dalhoff Bruhn ◽

Colin A. Stedmon ◽

Jérôme Comte ◽

Atsushi Matsuoka ◽

Neik Jesse Speetjens ◽

...

Keyword(s):

Organic Matter ◽

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Relative Abundance ◽

Microbial Community Composition ◽

The Arctic ◽

Glacial Deposit ◽

Deposit Type ◽

Lacustrine Deposit

Climate warming is accelerating erosion rates along permafrost-dominated Arctic coasts. To study the impact of erosion on marine microbial community composition and growth in the Arctic coastal zone, dissolved organic matter (DOM) from three representative glacial landscapes (fluvial, lacustrine and moraine) along the Yukon coastal plain, are provided as substrate to marine bacteria using a chemostat setup. Our results indicate that chemostat cultures with a flushing rate of approximately a day provide comparable DOM bioavailability estimates to those from bottle experiments lasting weeks to months. DOM composition (inferred from UV-Visible spectroscopy) and biodegradability (inferred from DOC concentration, bacterial production and respiration) significantly differed between the three glacial deposit types. DOM from fluvial and moraine deposit types shows more terrestrial characteristics with lower aromaticity (SR: 0.63 (&#177;0.02), SUVA254: 1.65 (&#177;0.06) respectively SR: 0.68 (&#177;0.00), SUVA254: 1.17 (&#177;0.06)) compared to the lacustrine deposit type (SR: 0.71 (&#177;0.02), SUVA254: 2.15 (&#177;0.05)). The difference in composition of DOM corresponds with the development of three distinct microbial communities, with a dominance of Alphaproteobacteria for fluvial and lacustrine deposit types (relative abundance 0.67 and 0.87 respectively) and a dominance of Gammaproteobacteria for moraine deposit type (relative abundance 0.88). Bacterial growth efficiency (BGE) is 66% for moraine-derived DOM, while 13% and 28% for fluvial-derived and lacustrine-derived DOM respectively. The three microbial communities therefore differ in their net effect on DOM utilization. The higher BGE value for moraine-derived DOM was found to be due to a larger proportion of labile colourless DOM. The results from this study, therefore indicate a substrate control of marine microbial community composition and activities, suggesting that the effect of permafrost thaw and erosion in the Arctic coastal zone will depend on subtle differences in DOM related to glacial deposit types. These differences further determines the speed and extent of DOM mineralization and thereby carbon channelling into biomass in the microbial food web. We therefore conclude that marine microbes strongly respond to the input of terrestrial DOM released during coastal erosion of Arctic glacial landscapes.

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Viewing soil systems from the top-down can make microbial ecology predictive for ecosystem functions

10.5194/egusphere-egu2020-3414 ◽

2020 ◽

Author(s):

Johannes Rousk ◽

Lettice Hicks

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Functional Response ◽

Community Composition ◽

Ecosystem Function ◽

Response Curve ◽

Ecosystem Processes ◽

Ecosystem Functions ◽

Top Down

Understanding the role of ecological communities in maintaining multiple ecosystem processes is a central challenge in ecology. Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial processes to community structure.Here, we propose a new conceptual framework to determine how microbial communities influence ecosystem processes, by applying a &#8220;top-down&#8221; approach. Looking from the &#8220;top&#8221;, we first view the microbial community associated with a specific function as a whole, and describe the dependence of microbial community processes on environmental factors (e.g. the intrinsic temperature dependence of bacterial growth rates), allowing us to define the aggregate functional response curve of the community. We then demonstrate that the whole community contribution to ecosystem function can be predicted, by parameterising the functional response curve with current environmental conditions. In a final step, we show how this functional information can be linked to the taxonomic community composition (amplicon assessments of microbial community composition) in order to identify &#8220;biomarker&#8221; taxa that capture microbial communities&#8217; regulation of ecosystem processes and the susceptibility of microbial community structure and function to environmental change. Ultimately, these biomarkers may be used as a diagnostic tool, enabling predictions of ecosystem function from community composition information combined with environmental metadata.

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Short-Term Effects of Different Forest Management Methods on Soil Microbial Communities of a Natural Quercus aliena var. acuteserrata Forest in Xiaolongshan, China

Forests ◽

10.3390/f10020161 ◽

2019 ◽

Vol 10 (2) ◽

pp. 161 ◽

Cited By ~ 4

Author(s):

Pan Wan ◽

Gongqiao Zhang ◽

Zhonghua Zhao ◽

Yanbo Hu ◽

Wenzhen Liu ◽

...

Keyword(s):

Microbial Community ◽

Forest Management ◽

Bacterial Community ◽

Microbial Communities ◽

Relative Abundance ◽

Fungal Community ◽

Soil Microbial Community ◽

Soil Microbial Communities ◽

Short Term ◽

Soil Microbial

One of the aims of sustainable forest management is to preserve the diversity and resilience of ecosystems. Unfortunately, changes in the soil microbial communities after forest management remain unclear. We analyzed and compared the soil microbial community of a natural Quercus aliena var. acuteserrata forest after four years of four different management methods using high-throughput sequencing technology. The forest management methods were close-to-nature management (CNFM), structure-based forest management (SBFM), secondary forest comprehensive silviculture (SFCS) and unmanaged control (CK). The results showed that: (1) the soil microbial community diversity indices were not significantly different among the different management methods. (2) The relative abundance of Proteobacteria in the SBFM treatment was lower than in the CK treatment, while the relative abundance of Acidobacteria in the SBFM was significantly higher than that in the CK treatment. The relative abundance of Ascomycota was highest in the CNFM treatment, and that of Basidiomycota was lowest in the CNFM treatment. However, the relative abundance of dominant bacterial and fungal phyla was not significantly different in CK and SFCS. (3) Redundancy analysis (RDA) showed that the soil organic matter (SOM), total nitrogen (TN), and available nitrogen (AN) significantly correlated with the bacterial communities, and the available potassium (AK) was the only soil nutrient, which significantly correlated with the composition of the fungal communities. The short-term SBFM treatment altered microbial bacterial community compositions, which may be attributed to the phyla present (e.g., Proteobacteria and Acidobacteria), and the short-term CNFM treatment altered microbial fungal community compositions, which may be attributed to the phyla present (e.g., Ascomycota and Basidiomycota). Furthermore, soil nutrients could affect the dominant soil microbial communities, and its influence was greater on the bacterial community than on the fungal community.

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Microbiome variation during culture growth of the European house dust mite, Dermatophagoides pteronyssinus

FEMS Microbiology Ecology ◽

10.1093/femsec/fiab039 ◽

2021 ◽

Vol 97 (4) ◽

Author(s):

Marta Nesvorna ◽

Stano Pekar ◽

Elena Shcherbachenko ◽

Vit Molva ◽

Tomas Erban ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Relative Abundance ◽

Environmental Samples ◽

Dermatophagoides Pteronyssinus ◽

Dust Mite ◽

Mite Density ◽

Culture Environment ◽

Culture Growth

ABSTRACT In culture, the house dust mite, Dermatophagoides pteronyssinus, shows different growth patterns, but the composition and changes in the associated microbial community during mite culture growth are poorly known. In this study, we analyzed temporal changes in microbial communities including ‘internal’ communities (inside mites, ingested) and ‘environmental’ communities (from culture environment). Microbial community structure was correlated with guanine content (a nitrogenous waste product of mites) and mite population density. Both internal and environmental microbial communities were remarkably consistent between biological replicates from the same culture age group and were composed of relatively few dominant taxa–11 bacterial and 3 fungal operational taxonomic units (OTUs). Significant changes over time in microbial community structure in the bulk culture environment and in internal mite samples were observed. The yeast, Saccharomyces cerevisiae, a main component of the mite diet, gradually disappeared during mite culture growth and was replaced by fungi from the genera Aspergillus and Candida in both ‘internal’ and ‘environmental’ samples. In environmental samples, bacteria from the genus Lactobacillus and S. cerevisiae were negatively correlated, and Aspergillus and Candida positively correlated, with guanine content. The relative abundance of bacteria from the genus Kocuria increased with mite density but declined with increasing guanine content. The relative abundance of bacteria from the genus Virgibacillus was negatively correlated with mite density in ‘internal’ samples. Gram-positive bacteria dominated bacterial microbiomes at all time points in our experiments, indicating a more limited possibility for vaccine contamination by bacterial endotoxins (heat-stable lipopolysaccharides produced mostly by Gram-negative bacteria) in our experimental cultures.

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Microbial communities in an ultra-oligotrophic sea are more affected by season than by distance from shore

10.1101/2020.04.17.044305 ◽

2020 ◽

Author(s):

Markus Haber ◽

Dalit Roth Rosenberg ◽

Maya Lalzar ◽

Ilia Burgsdorf ◽

Kumar Saurav ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Mediterranean Sea ◽

Community Composition ◽

Eastern Mediterranean ◽

Microbial Community Composition ◽

Eastern Mediterranean Sea ◽

South Eastern ◽

Structure And Activity

AbstractMarine microbial communities vary seasonally and spatially, but these two factors are rarely addressed together. We studied temporal and spatial patterns of the microbial community structure and activity along a coast to offshore transect from the Israeli coast of the Eastern Mediterranean Sea (EMS) over six cruises, in three seasons of two consecutive years. The ultra-oligotrophic status of the South Eastern Mediterranean Sea was reflected in the microbial community composition that was dominated by oligotrophic microbial groups such as SAR11 throughout the year, even at the most coastal station sampled. Seasons affected microbial communities much more than distance from shore explaining about half of the observed variability in the microbial community, compared to only about 6% that was explained by station. However, the most coastal site differed significantly in community structure and activity from the three further offshore stations in early winter and summer, but not in spring. Our data on the microbial community composition and its seasonality from a transect into the South Eastern Levantine basin support the notion that the EMS behaves similar to open gyres rather than an inland sea.

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Slope aspect influences soil microbial community structure and composition in the Israel arid Mediterranean

Israel Journal of Ecology and Evolution ◽

10.1163/22244662-bja10008 ◽

2020 ◽

pp. 1-6

Author(s):

I. Moroenyane ◽

B.M. Tripathi ◽

J.M. Adams ◽

S. Chen ◽

Y. Steinberger

Keyword(s):

Organic Matter ◽

Soil Moisture ◽

Community Structure ◽

Microbial Community ◽

Microbial Diversity ◽

Community Composition ◽

Mediterranean Ecosystems ◽

Slope Aspect ◽

Diversity Patterns ◽

Composition And Structure

Microbial biogeographical patterns in Mediterranean ecosystems are becoming widely documented; however, the influences of slope aspect on the microbial community composition and structure are poorly understood. This study tested the hypotheses that slope aspect and organic matter content would influence microbial diversity patterns and distribution. Sets of five soil samples were collected from different slope aspects (north slope, south slopes, and valley bottom) and bacterial and fungal communities were examined using the 16S rRNA gene and ITS1 region sequencing, respectively, on the Illumina HiSeq platform. Organic matter and soil moisture varied significantly across all sites but did not influence microbial diversity patterns. Community structure (Bray-Curtis dissimilarity) indicated that each site had a distinct microbial community, and soil moisture along with organic matter modulated the community structure. Relative abundance of key bacterial taxa (Actinobacteria and Bacteriodetes ) and fungal taxa (Ascomycota was significantly influenced by slope aspect. Our results show, for the first time, that the often reported slope aspect dynamics of the soil microbiomes do in fact influence bacterial and fungal community composition and structure. Overall, taken together with previous studies from the region, this study provides novel insight on the physio-chemical properties that modulate the biogeographical patterns of soil microbes and contributes to our knowledge of factors that mediate microbial ecology in Mediterranean ecosystems.

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The effects of soil depth on the structure of microbial communities in agricultural soils in Iowa, USA

10.1101/2020.03.31.018416 ◽

2020 ◽

Author(s):

Jingjie Hao ◽

Yen Ning Chai ◽

Raziel A. Ordóñez ◽

Emily E. Wright ◽

Sotirios Archontoulis ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Bacterial Community ◽

Microbial Communities ◽

Community Composition ◽

Microbial Community Structure ◽

Soil Depth ◽

Bacterial Community Composition ◽

Soil Microbial Communities ◽

Soil Microbial

AbstractThe determination of how microbial community structure changes within the soil profile, will be beneficial to understanding the long-term health of agricultural soil ecosystems and will provide a first step towards elucidating how deep soil microbial communities contribute to carbon sequestration. This study aimed to investigate the differences in the microbial community abundance, composition and diversity throughout from the surface layers down to deep soils in corn and soybean fields in Iowa, USA. We used 16S rRNA amplicon sequencing of soil samples to characterize the change in microbial community structure. Our results revealed decreased richness and diversity in bacterial community structure with increasing soil depth. We also observed distinct distribution patterns of bacterial community composition along soil profiles. Soil and root data at different depths enabled us to demonstrate that the soil organic matter, soil bulk density and plant water availability were all significant factors in explaining the variation in soil microbial community composition. Our findings provide valuable insights in the changes in microbial community structure to depths of 180 cm in one of the most productive agricultural regions in the world. This knowledge will be important for future management and productivity of agroecosystems in the face of increasing demand for food and climate change.

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Soil microbial community composition in a paddy field with different fertilization managements

Canadian Journal of Microbiology ◽

10.1139/cjm-2020-0590 ◽

2021 ◽

pp. 1-11

Author(s):

Limin Wang ◽

Dongfeng Huang

Keyword(s):

Community Structure ◽

Microbial Community ◽

Soil Properties ◽

Microbial Communities ◽

Community Composition ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Phosphorus Fertilization ◽

Bacterial Phyla ◽

P Fertilizer

Microbes play vital roles in soil quality; however, their response to N (nitrogen) and P (phosphorus) fertilization in acidic paddy soils of subtropical China remains poorly understood. Here, a 10-year field experiment was conducted to evaluate the effects of different fertilization treatments on microbial communities by Illumina MiSeq sequencing. The results showed that different fertilization treatments did not exert a significant effect on microbial alpha diversity, but altered soil properties, and thus affected microbial community composition. The microbial communities in the T1 (optimized N and P fertilizer) and T2 (excessive N fertilizer) treated soils differed from those in the T0 (no N and P fertilizer) and T3 (excessive P fertilizer) treated soils. In addition, the bacterial phyla Proteobacteria, Chloroflexi, and Acidobacteria, and the fungal phyla Ascomycota and Basidiomycota dominated all the fertilized treatments. Soil total potassium (TK) concentration was the most important factor driving the variation in bacterial community structure under different fertilization regimes, while the major factors shaping fungal community structure were soil TN and NO3–-N (nitrate N). These findings indicate that optimization of N and P application rates might result in variations in soil properties, which changed the microbial community structure in the present study.

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Passive Treatment for Acid Mine Drainage Partially Restores Microbial Community Structure in Different Stream Habitats

Water ◽

10.3390/w13223300 ◽

2021 ◽

Vol 13 (22) ◽

pp. 3300

Author(s):

Alexis N. Neff ◽

Dean M. DeNicola ◽

Chris Maltman

Keyword(s):

Community Structure ◽

Microbial Community ◽

Acid Mine Drainage ◽

Microbial Communities ◽

Community Composition ◽

Microbial Community Structure ◽

Mine Drainage ◽

Microbial Community Composition ◽

Taxonomic Composition ◽

Passive Treatment

The assessment of the degree to which biological communities in streams impaired by acid mine drainage (AMD) are restored by passive treatment has focused primarily on eukaryotic-cell organisms and microbial processes. The responses of microbial community structure to passive treatment have received much less attention, even though functional processes such as nutrient cycling and organic matter decomposition depend on taxonomic composition. Our objective was to determine the degree to which passive treatment restored microbial communities in three types of habitats: aqueous, leaf, and sediment. To assess their recovery, we compared the community composition in these habitats based on 16S rRNA gene sequencing at three different stream sites: an untreated AMD site (U), a remediated site below AMD passive treatment (T), and an unimpaired reference site (R). The acidity, conductivity, and soluble metal concentrations at T were found to be elevated compared to R, but generally 1–2 orders of magnitude less than at U. Microbial community composition was found to be synergistically affected by habitat type and AMD impact, with the similarity among communities in the three habitats increasing with the severity of the AMD. Sediment- and leaf-associated microbial communities at U were characterized by taxa that are tolerant to severe AMD. The absence of the nitrogen oxidizing bacterium Nitrospira in sediment communities at T and U was found to correspond to higher NH4+ concentrations compared to R, possibly because of the presence of iron oxyhydroxide precipitate. In contrast, the microbial composition was found to be similar between the T and R sites for both aqueous and leaf communities, indicating that passive treatment was more able to restore these communities to the reference condition than sediment communities. The remediation of AMD streams should consider the habitat-specific responses of microbial community composition and be guided by future studies that empirically couple changes in taxonomic composition to measured functional processes.

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