scholarly journals Linking Microbial Community Structure to Trait Distributions and Functions Using Salinity as an Environmental Filter

mBio ◽  
2019 ◽  
Vol 10 (4) ◽  
Author(s):  
Kristin M. Rath ◽  
Arpita Maheshwari ◽  
Johannes Rousk
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Salt Tolerance ◽  
Microbial Communities ◽  
Bacterial Growth ◽  
Soil Microbes ◽  
Fungal Growth ◽  
Environmental Filter ◽  
Trait Distribution ◽  
Nonsaline Soil

ABSTRACT The structure and function of microbial communities vary along environmental gradients; however, interlinking the two has been challenging. In this study, salinity was used as an environmental filter to study how it could shape trait distributions, community structures, and the resulting functions of soil microbes. The environmental filter was applied by salinizing nonsaline soil (0 to 22 mg NaCl g−1). Our targeted community trait distribution (salt tolerance) was determined with dose-response relationships between bacterial growth and salinity. The bacterial community structure responses were resolved with Illumina 16S rRNA gene amplicon sequencing, and the microbial functions determined were respiration and bacterial and fungal growth. Salt exposure quickly resulted in filtered trait distributions, and stronger filters resulted in larger shifts. The filtered trait distributions correlated well with community composition differences, suggesting that trait distribution shifts were driven at least partly by species turnover. While salt exposure decreased respiration, microbial growth responses appeared to be characterized by competitive interactions. Fungal growth was highest when bacterial growth was inhibited by the highest salinity, and it was lowest when the bacterial growth rate peaked at intermediate salt levels. These findings corroborated a higher potential for fungal salt tolerance than bacterial salt tolerance for communities derived from a nonsaline soil. In conclusion, by using salt as an environmental filter, we could interlink the targeted trait distribution with both the community structure and resulting functions of soil microbes. IMPORTANCE 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 composition and structure. Here, we apply a conceptual framework to determine how microbial communities influence ecosystem processes, by applying a “top-down” trait-based approach. By determining the dependence of microbial processes on environmental factors (e.g., the tolerance to salinity), we can define the aggregate response trait distribution of the community, which then can be linked to the community structure and the resulting function performed by the microbial community.

Effects of simulated drought and warming on microbial responses to drying and rewetting in contrasting land-uses

2020 ◽  
Author(s):  
Ainara Leizeaga ◽  
Lettice C. Hicks ◽  
Albert C. Brangarí ◽  
Menale Wondie ◽  
Hans Sandén ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Growth ◽  
Forest Soils ◽  
Fungal Growth ◽  
Land Uses ◽  
Soil Microbial ◽  
Drying And Rewetting ◽  
Microbial Responses ◽  
Simulated Drought

<p>Climate change will increase temperatures and the frequency and intensity of extreme drought and rainfall events. When a drought period is followed by a rainfall event, there is a big CO<sub>2</sub> pulse from soil to the atmosphere which is regulated by soil microorganisms. In the present study, we set out to investigate how simulated drought and warming affects the soil microbial responses to drying and rewetting (DRW), and how those responses will interact with the level of land degradation. Previous work has shown that exposure DRW cycles in the laboratory and in the field can induce changes in the microbial community such that it resumes growth rates faster after a DRW cycle. In addition, it has been observed that a history of drought in both a humid heathland ecosystem in Northern Europe and in semi-arid grasslands in Texas can select for microorganisms with a higher carbon use efficiency (CUE) during DRW. In this study we tested if these observations could be extended to subtropical environments.</p><p>Rain shelters and open top chambers (OTC) were installed in Northwestern Ethiopia in two contrasting land-uses; a degraded cropland and a pristine forest. Soils were sampled (>1-year field treatments) and exposed to a DRW cycle in the laboratory. Microbial growth and respiration responses were followed with high temporal resolution over 3 weeks. We hypothesized that (i) simulated drought would result in more resilient and efficient microbial communities to DRW, while (ii) simulated warming should leave microbial community traits linked to moisture unchanged. In addition, (iii) we hypothesized that microbial communities would recover growth rates faster in the cropland since that ecosystem is more prone to DRW events.</p><p>Microbial responses in both land-uses and treatments universally showed a highly resilient type of community response with both bacterial growth and fungal growth increasing immediately upon rewetting, linked with the expected respiration pulse. The field treatments simulating drought and warming did not affect the already high resilience of soil microbial communities to DRW cycles. However, differences between the rates of recovery between fungi and bacteria were observed. Fungal growth recovered faster than bacterial growth, peaking c. 15 h in comparison to bacteria that peaked at c.20h after rewetting. Simulated drought reduced the microbial CUE during rewetting in croplands without affecting the forest soils. The CUE was also elevated in the warming treatments in both land-uses, and generally higher in croplands than in forest soils. Taken together, the responses in microbial CUE during the rewetting of dry soils were likely linked to either (i) differences in resource availability which were higher in warming treatments and in croplands compared to forests, or (ii) selection of  more efficient microbial communities due to a higher exposure to DRW events driven by the higher temperatures in the cropland, and increased evapotranspiration in the warming treatments.</p><div> <div> <div> </div> </div> </div>

Phylum-Specific Primer Design and Implication in Quantification of the Microbial Community Structure in GuJingGong Pit Mud

2014 ◽  
Vol 1051 ◽  
pp. 311-316 ◽  
Author(s):  
Xi Mei Luo ◽  
Zhi Lei Gao ◽  
Hui Min Zhang ◽  
An Jun Li ◽  
Hong Kui He ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Real Time Quantitative Pcr ◽  
Sequencing Technologies ◽  
Specific Pcr ◽  
Pit Mud ◽  
Almost All ◽  
Polymerase Chain Reaction Primers

In recent years, despite the significant improvement of sequencing technologies such as the pyrosequencing, rapid evaluation of microbial community structures remains very difficult because of the abundance and complexity of organisms in almost all natural microbial communities. In this paper, a group of phylum-specific primers were elaborately designed based on a single nucleotide discrimination technology to quantify the main microbial community structure from GuJingGong pit mud samples using the real-time quantitative PCR (qPCR). Specific PCR (polymerase chain reaction) primers targeting a particular group would provide promising sensitivity and more in-depth assessment of microbial communities.

scholarly journals High-throughput amplicon sequencing reveals the spatiotemporal effects, abiotic and biotic shaping factors for the microbial communities in tropical mangrove sediments in Sanya, China

2020 ◽  
Author(s):  
Wu Qu ◽  
Boliang Gao ◽  
Jie Wu ◽  
Min Jin ◽  
Jianxin Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Fungal Community ◽  
Amplicon Sequencing ◽  
Biotic Factors ◽  
Community Structures ◽  
Mangrove Sediments ◽  
Element Cycling ◽  
Microbial Community Structures

Abstract Background Microbial roles in element cycling and nutrient providing are crucial for mangrove ecosystems and serve as important regulators for climate change in Earth ecosystem. However, some key information about the spatiotemporal influences and abiotic and biotic shaping factors for the microbial communities in mangrove sediments remains lacking. Methods In this work, 22 sediment samples were collected from multiple spatiotemporal dimensions, including three locations, two depths, and four seasons, and the bacterial, archaeal, and fungal community structures in these samples were studied using amplicon sequencing. Results The microbial community structures were varied in the samples from different depths and locations based on the results of LDA effect size analysis, principal coordinate analysis, the analysis of similarities, and permutational multivariate ANOVA. However, these microbial community structures were stable among the seasonal samples. Linear fitting models and Mantel test showed that among the 13 environmental factors measured in this study, the sediment particle size (PS) was the key abiotic shaping factor for the bacterial, archaeal, or fungal community structure. Besides PS, salinity and humidity were also significant impact factors according to the canonical correlation analysis (p ≤ 0.05). Co-occurrence networks demonstrated that the bacteria assigned into phyla Ignavibacteriae, Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria were the key biotic factors for shaping the bacterial community in mangrove sediments. Conclusions This work showed the variability on spatial dimensions and the stability on temporal dimension for the bacterial, archaeal, or fungal microbial community structure, indicating that the tropical mangrove sediments are versatile but stable environments. PS served as the key abiotic factor could indirectly participate in material circulation in mangroves by influencing microbial community structures, along with salinity and humidity. The bacteria as key biotic factors were found with the abilities of photosynthesis, polysaccharide degradation, or nitrogen fixation, which were potential indicators for monitoring mangrove health, as well as crucial participants in the storage of mangrove blue carbons and mitigation of climate warming. This study expanded the knowledge of mangroves for the spatiotemporal variation, distribution, and regulation of the microbial community structures, thus further elucidating the microbial roles in mangrove management and climate regulation.

scholarly journals Towards a function-first framework to make soil microbial ecology predictive

2021 ◽  
Author(s):  
Johannes Rousk ◽  
Lettice Hicks
Keyword(s):  
Microbial Community ◽  
Environmental Factors ◽  
Microbial Communities ◽  
Functional Response ◽  
Community Composition ◽  
Ecosystem Function ◽  
Bacterial Growth ◽  
Response Curve ◽  
Ecosystem Functions ◽  
Soil Microbial

<p>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 function to community composition and structure. Here, we propose a function-first framework to predict how microbial communities influence ecosystem functions.</p><p>We first view the microbial community associated with a specific function as a whole, and describe the dependence of microbial functions on environmental factors (e.g. the intrinsic temperature dependence of bacterial growth rates). This step defines the aggregate functional response curve of the community. Second, the contribution of the whole community to ecosystem function can be predicted, by combining the functional response curve with current environmental conditions. Functional response curves can then be linked with taxonomic data in order to identify sets of “biomarker” taxa that signal how microbial communities regulate ecosystem functions. Ultimately, such indicator taxa may be used as a diagnostic tool, enabling predictions of ecosystem function from community composition.</p><p>In this presentation, we provide three examples to illustrate the proposed framework, whereby the dependence of bacterial growth on environmental factors, including temperature, pH and salinity, is defined as the functional response curve used to interlink soil bacterial community structure and function. Applying this framework will make it possible to predict ecosystem functions directly from microbial community composition.</p>

scholarly journals Agricultural Pollution Risks Influence Microbial Ecology in Honghu Lake

2018 ◽  
Author(s):  
Maozhen Han ◽  
Melissa Dsouza ◽  
Chunyu Zhou ◽  
Hongjun Li ◽  
Junqian Zhang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Physicochemical Properties ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
Agricultural Pollution ◽  
Agricultural Activities ◽  
Sediment Samples ◽  
Water And Sediment ◽  
Honghu Lake

AbstractBackgroundAgricultural activities, such as stock-farming, planting industry, and fish aquaculture, can influence the physicochemistry and biology of freshwater lakes. However, the extent to which these agricultural activities, especially those that result in eutrophication and antibiotic pollution, effect water and sediment-associated microbial ecology, remains unclear.MethodsWe performed a geospatial analysis of water and sediment associated microbial community structure, as well as physicochemical parameters and antibiotic pollution, across 18 sites in Honghu lake, which range from impacted to less-impacted by agricultural pollution. Furthermore, the co-occurrence network of water and sediment were built and compared accorded to the agricultural activities.ResultsPhysicochemical properties including TN, TP, NO3--N, and NO2--N were correlated with microbial compositional differences in water samples. Likewise, in sediment samples, Sed-OM and Sed-TN correlated with microbial diversity. Oxytetracycline and tetracycline concentration described the majority of the variance in taxonomic and predicted functional diversity between impacted and less-impacted sites in water and sediment samples, respectively. Finally, the structure of microbial co-associations was influenced by the eutrophication and antibiotic pollution.ConclusionThese analyses of the composition and structure of water and sediment microbial communities in anthropologically-impacted lakes are imperative for effective environmental pollution monitoring. Likewise, the exploration of the associations between environmental variables (e.g. physicochemical properties, and antibiotics) and community structure is important in the assessment of lake water quality and its ability to sustain agriculture. These results show agricultural practices can negatively influence not only the physicochemical properties, but also the biodiversity of microbial communities associated with the Honghu lake ecosystem. And these results provide compelling evidence that the microbial community can be used as a sentinel of eutrophication and antibiotics pollution risk associated with agricultural activity; and that proper monitoring of this environment is vital to maintain a sustainable environment in Honghu lake.

A quantitative comparison of microbial community structure of estuarine sediments from microcosms and the field

1986 ◽  
Vol 32 (4) ◽  
pp. 319-325 ◽  
Author(s):  
Thomas W. Federle ◽  
Robert J. Livingston ◽  
Loretta E. Wolfe ◽  
David C. White
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Ecological Factors ◽  
Estuarine Sediments ◽  
Physical Factors ◽  
Multivariate Statistical ◽  
Apalachicola Bay ◽  
Sound Experiment

Estuarine soft-bottom sediments in microcosms and the field were compared with regard to microbial community structure. Community structure was determined by analyzing the fatty acids derived from the microbial lipids in the sediments. Fatty acid profiles were compared using a multivariate statistical approach. Experiments were performed using sediments from St. George Sound and Apalachicola Bay, Florida. The community structure of St. George Sound sediments was apparently controlled by epibenthic predators. In Apalachicola Bay, the dominant influences were physical factors related to the flow of the Apalachicola River. In the St. George Sound experiment, microbial communities in the microcosms differed from those in the field after only 2 weeks, and the degree of this difference increased substantially as time progressed. In the Apalachicola Bay experiment, although microbial communities in the microcosms were detectably different from those in the field, the degree of this difference was not large nor did it increase with time. This differential behavior of sediment communities from different sites may be related to the different ecological factors regulating community composition at these sites.

scholarly journals Microbial community structure in the western tropical South Pacific

2018 ◽  
Vol 15 (12) ◽  
pp. 3909-3925 ◽  
Author(s):  
Nicholas Bock ◽  
France Van Wambeke ◽  
Moïra Dion ◽  
Solange Duhamel
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
N2 Fixation ◽  
Phytoplankton Biomass ◽  
South Pacific ◽  
Global Ocean ◽  
Bottom Up

Abstract. Oligotrophic regions play a central role in global biogeochemical cycles, with microbial communities in these areas representing an important term in global carbon budgets. While the general structure of microbial communities has been well documented in the global ocean, some remote regions such as the western tropical South Pacific (WTSP) remain fundamentally unexplored. Moreover, the biotic and abiotic factors constraining microbial abundances and distribution remain not well resolved. In this study, we quantified the spatial (vertical and horizontal) distribution of major microbial plankton groups along a transect through the WTSP during the austral summer of 2015, capturing important autotrophic and heterotrophic assemblages including cytometrically determined abundances of non-pigmented protists (also called flagellates). Using environmental parameters (e.g., nutrients and light availability) as well as statistical analyses, we estimated the role of bottom–up and top–down controls in constraining the structure of the WTSP microbial communities in biogeochemically distinct regions. At the most general level, we found a “typical tropical structure”, characterized by a shallow mixed layer, a clear deep chlorophyll maximum at all sampling sites, and a deep nitracline. Prochlorococcus was especially abundant along the transect, accounting for 68 ± 10.6 % of depth-integrated phytoplankton biomass. Despite their relatively low abundances, picophytoeukaryotes (PPE) accounted for up to 26 ± 11.6 % of depth-integrated phytoplankton biomass, while Synechococcus accounted for only 6 ± 6.9 %. Our results show that the microbial community structure of the WTSP is typical of highly stratified regions, and underline the significant contribution to total biomass by PPE populations. Strong relationships between N2 fixation rates and plankton abundances demonstrate the central role of N2 fixation in regulating ecosystem processes in the WTSP, while comparative analyses of abundance data suggest microbial community structure to be increasingly regulated by bottom–up processes under nutrient limitation, possibly in response to shifts in abundances of high nucleic acid bacteria (HNA).

scholarly journals Microbial community structure and the relationship with soil carbon and nitrogen in an original Korean pine forest of Changbai Mountain, China

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Minghui Liu ◽  
Xin Sui ◽  
Yanbo Hu ◽  
Fujuan Feng
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Microbial Community Structure ◽  
Soil Microbes ◽  
Mixed Forest ◽  
Korean Pine ◽  
Soil Microbial ◽  
The Relationship ◽  
Main Factor

Abstract Background The broad-leaved Korean pine mixed forest is an important and typical component of a global temperate forest. Soil microbes are the main driver of biogeochemical cycling in this forest ecosystem and have complex interactions with carbon (C) and nitrogen (N) components in the soil. Results We investigated the vertical soil microbial community structure in a primary Korean pine-broadleaved mixed forest in Changbai Mountain (from 699 to 1177 m) and analyzed the relationship between the microbial community and both C and N components in the soil. The results showed that the total phospholipid fatty acid (PLFA) of soil microbes and Gram-negative bacteria (G-), Gram-positive bacteria (G+), fungi (F), arbuscular mycorrhizal fungi (AMF), and Actinomycetes varied significantly (p < 0.05) at different sites (elevations). The ratio of fungal PLFAs to bacterial PLFAs (F/B) was higher at site H1, and H2. The relationship between microbial community composition and geographic distance did not show a distance-decay pattern. The coefficients of variation for bacteria were maximum among different sites (elevations). Total soil organic carbon (TOC), total nitrogen (TN), soil water content (W), and the ratio of breast-height basal area of coniferous trees to that of broad-leaved tree species (RBA) were the main contributors to the variation observed in each subgroup of microbial PLFAs. The structure equation model showed that TOC had a significant direct effect on bacterial biomass and an indirect effect upon bacterial and fungal biomass via soil readily oxidized organic carbon (ROC). No significant relationship was observed between soil N fraction and the biomass of fungi and bacteria. Conclusion The total PLFAs (tPLFA) and PLFAs of soil microbes, including G-, G+, F, AMF, and Actinomycetes, were significantly affected by elevation. Bacteria were more sensitive to changes in elevation than other microbes. Environmental heterogeneity was the main factor affecting the geographical distribution pattern of microbial community structure. TOC, TN, W and RBA were the main driving factors for the change in soil microbial biomass. C fraction was the main factor affecting the biomass of fungi and bacteria and ROC was one of the main sources of the microbial-derived C pool.

scholarly journals Defining the Core Citrus Leaf- and Root-Associated Microbiota: Factors Associated with Community Structure and Implications for Managing Huanglongbing (Citrus Greening) Disease

2017 ◽  
Vol 83 (11) ◽  
Author(s):  
Ryan A. Blaustein ◽  
Graciela L. Lorca ◽  
Julie L. Meyer ◽  
Claudio F. Gonzalez ◽  
Max Teplitski
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Illumina Sequencing ◽  
Symptom Severity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
The Core ◽  
Symptom Progression

ABSTRACTStable associations between plants and microbes are critical to promoting host health and productivity. The objective of this work was to test the hypothesis that restructuring of the core microbiota may be associated with the progression of huanglongbing (HLB), the devastating citrus disease caused byLiberibacter asiaticus,Liberibacter americanus, andLiberibacter africanus. The microbial communities of leaves (n= 94) and roots (n= 79) from citrus trees that varied by HLB symptom severity, cultivar, location, and season/time were characterized with Illumina sequencing of 16S rRNA genes. The taxonomically rich communities contained abundant core members (i.e., detected in at least 95% of the respective leaf or root samples), some overrepresented site-specific members, and a diverse community of low-abundance variable taxa. The composition and diversity of the leaf and root microbiota were strongly associated with HLB symptom severity and location; there was also an association with host cultivar. The relative abundance ofLiberibacterspp. among leaf microbiota positively correlated with HLB symptom severity and negatively correlated with alpha diversity, suggesting that community diversity decreases as symptoms progress. Network analysis of the microbial community time series identified a mutually exclusive relationship betweenLiberibacterspp. and members of theBurkholderiaceae,Micromonosporaceae, andXanthomonadaceae. This work confirmed several previously described plant disease-associated bacteria, as well as identified new potential implications for biological control. Our findings advance the understanding of (i) plant microbiota selection across multiple variables and (ii) changes in (core) community structure that may be a precondition to disease establishment and/or may be associated with symptom progression.IMPORTANCEThis study provides a comprehensive overview of the core microbial community within the microbiomes of plant hosts that vary in extent of disease symptom progression. With 16S Illumina sequencing analyses, we not only confirmed previously described bacterial associations with plant health (e.g., potentially beneficial bacteria) but also identified new associations and potential interactions between certain bacteria and an economically important phytopathogen. The importance of core taxa within broader plant-associated microbial communities is discussed.

scholarly journals Vertebrate Decomposition Is Accelerated by Soil Microbes

2014 ◽  
Vol 80 (16) ◽  
pp. 4920-4929 ◽  
Author(s):  
Christian L. Lauber ◽  
Jessica L. Metcalf ◽  
Kyle Keepers ◽  
Gail Ackermann ◽  
David O. Carter ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Soil Microbes ◽  
Soil Microbial Communities ◽  
Natural Phenomenon ◽  
Rrna Gene ◽  
Data Set ◽  
Soil Microbial ◽  
Decomposer Community ◽  
Carrion Decomposition

ABSTRACTCarrion decomposition is an ecologically important natural phenomenon influenced by a complex set of factors, including temperature, moisture, and the activity of microorganisms, invertebrates, and scavengers. The role of soil microbes as decomposers in this process is essential but not well understood and represents a knowledge gap in carrion ecology. To better define the role and sources of microbes in carrion decomposition, lab-reared mice were decomposed on either (i) soil with an intact microbial community or (ii) soil that was sterilized. We characterized the microbial community (16S rRNA gene for bacteria and archaea, and the 18S rRNA gene for fungi and microbial eukaryotes) for three body sites along with the underlying soil (i.e., gravesoils) at time intervals coinciding with visible changes in carrion morphology. Our results indicate that mice placed on soil with intact microbial communities reach advanced stages of decomposition 2 to 3 times faster than those placed on sterile soil. Microbial communities associated with skin and gravesoils of carrion in stages of active and advanced decay were significantly different between soil types (sterile versus untreated), suggesting that substrates on which carrion decompose may partially determine the microbial decomposer community. However, the source of the decomposer community (soil- versus carcass-associated microbes) was not clear in our data set, suggesting that greater sequencing depth needs to be employed to identify the origin of the decomposer communities in carrion decomposition. Overall, our data show that soil microbial communities have a significant impact on the rate at which carrion decomposes and have important implications for understanding carrion ecology.

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