Barrier-Free Microhabitats: Self-Organized Seclusion in Microbial Communities

PurposeWe determined the microbial community diversity and structure in soil samples under different amounts of biochar added. Meanwhile, we also researched the relationships between soil microbial and soil physicochemical properties.MethodIn this study, a field experiment was set up, with a total of three experimental treatments: no biochar application, 10 t/m3 biochar application, and 20 t/m3 application. High-throughput sequencing technologies were used for soil samples of different treatment groups to understand soil microbial diversity and community structure.ResultsWe found that the soil physicochemical properties after biochar addition were better than those without biochar addition, and the alpha diversity was higher in biochar addition level of 20 t/m3 than other processing groups. Proteobacteria, Cyanobacteria, and Actinobacteria were the dominant phyla of this study. The dominant genera were Skermanella, Nostoc, Frankia, and Unclassified-p-protecbacteria. At the gate level, Actinobacteria had significant differences among the three groups with different addition amounts. The microbial community structure was mainly influenced by soil porosity, soil moisture content, nitrogen fertilizer, and potassium fertilizer other than soil phosphate fertilizer and organic matter.ConclusionsThe results suggested that changes under different amounts of biochar added generate changes in soil physicochemical properties and control the soil composition of microbial communities. This provides a new basis for soil improvement.

EDITORIAL article Front. Microbiol., 26 September 2014Sec. Terrestrial Microbiology Volume 5 - 2014 | https://doi.org/10.3389/fmicb.2014.00497

The mining industry in China plays a pivotal role in economic development but also leads to severe environmental issues, particularly heavy metal pollution in soils. Heavy metal pollution significantly impacts soil microbial communities due to its persistence and long-term residual effects. We assessed changes in microbial diversity, community structure, and assembly mechanisms in selenium-impacted soils. This study investigates the impacts of selenium (Se) and other heavy metals on soil microbial communities in selenium-rich mining areas using full-length 16S rRNA gene sequencing. Our results showed that Se and other heavy metal contamination significantly altered microbial community composition, favoring metal-tolerant phyla such as Proteobacteria, Actinobacteriota and Firmicutes, while reducing the abundance of sensitive groups like Acidobacteriota and Chloroflexi. Microbial diversity decreased as Se and other heavy metal concentrations increased. Mantel test analysis revealed that soil total potassium (TK), soil organic carbon, total nitrogen, and several other metals, including zinc, niobium, titanium (Ti), manganese, rubidium, barium, potassium, cobalt, gallium (Ga), Se, chromium (Cr), vanadium, and copper were significantly and positively correlated with microbial community composition across all soil samples. Random forest analysis showed that soil TK and multiple elements [Cr, Ti, nickel (Ni), Ga and Se] were the most important predictors of bacterial diversity, emphasizing the role of multiple elements in shaping microbial communities. Co-occurrence network analysis revealed that Se and other heavy metal contamination reduced network complexity and stability, with high Se-contaminated soils exhibiting fragmented microbial networks. Community assembly was primarily driven by drift in control soils, whereas dispersal limitation became more prominent in Se-contaminated soils due to heavy metal toxicity. These findings highlight the ecological consequences of heavy metal pollution on microbial communities and offer valuable insights for effective soil management and remediation strategies.

Evolution in changing seas.

Manipulation of the soil pore and microbial community structure in soil mesocosm incubation studies

Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach’s food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.

Soil salinization is one main environmental factor restricting plant growth and agricultural productivity. However, phytoremediation is one of the important means to improve saline-alkali soil by planting halophytes or salt-tolerant plants. In order to study whether there are differences among soil microorganisms in different phytoremediation, the effects of four plants, including alfalfa (MX), oil sunflower (YK), maize (YM) and ryegrass (HMC) on soil physicochemical properties, enzyme activity and microbial community diversity and composition were investigated in this study and the relationships between microbial community structure and soil physicochemical properties, enzyme activity were analyzed. The results showed that all plants treatments significantly decreased pH, TS (total saltinity) and BD (bulk density), while increased OM (organic matter), TN (total nitrogen), AN (available nitrogen), TP (total phosphorus), AP (available phosphorus), TK (total potassium) and TPOR (total porosity), and the number of nitrite bacteria reduced by planting at the same time. Except for YM, other treatments significantly increased the number of nitrifying and denitrifying bacteria compared with CK, while only YK increased that of fungi. Additionally, all plants increased the activity of nitrite reductase and decreased that of urease. More interestingly, plants treatments shifted microbial community compositions, and only YM significantly decreased the bacterial diversity and increased the fungal diversity. Redundancy analysis suggested that TK, pH, BD, TS, AN, OM and nitrite reductase, lignin peroxidase were the key environmental factors that shaped the bacterial community structure, while that of fungi was mainly driven by OM, nitrite reductase, urease and lignin peroxidase. The results indicated that MX and YM are the best choice for remediation of saline-alkali soil. These data can provide certain theoretical basis for the further restoration of saline-alkali land. HIGHLIGHTS The effects of different phytoremediation on microbial diversity and community structure were different. Phytoremediation can significantly decreased pH, TS and BD, while increased OM, TN, AN, TP, AP, TK and TPOR in saline-alkali soil. All plants increased the activity of nitrite reductase and decreased the activity of urease.

Microbial population size, production, diversity, and community structure are greatly influenced by the surrounding physicochemical conditions, such as large-scale biogeographic provinces and water masses. An oceanic mesoscale dipole consists of a cyclonic eddy and an anticyclonic eddy. Dipoles occur frequently in the ocean and usually last from a few days to several months; they have significant impacts on local and global oceanic biological, ecological, and geochemical processes. To better understand how dipoles shape microbial communities, we examined depth-resolved distributions of microbial communities across a dipole in the South China Sea. Our data demonstrated that the dipole had a substantial influence on microbial distributions, community structure, and functional groups both vertically and horizontally. Large alpha and beta diversity differences were observed between anticyclonic and cyclonic eddies in surface and subsurface layers, consistent with distribution changes of major bacterial groups in the dipole. The dipole created uplift, downward transport, enrichment, depletion, and horizontal transport effects. We also found that the edge of the dipole might induce strong subduction, indicated by the presence of Prochlorococcus and Synechococcus in deep waters. Our findings suggest that dipoles, with their unique characteristics, might act as a driver for microbial community dynamics.IMPORTANCE Oceanic dipoles, which consist of a cyclonic eddy and an anticyclonic eddy together, are among the most contrasted phenomena in the ocean. Dipoles generate strong vertical mixing and horizontal advection, inducing biological responses. This study provides vertical profiles of microbial abundance, diversity, and community structure in a mesoscale dipole. We identify the links between the physical oceanography and microbial oceanography and demonstrate that the dipole, with its unique features, could act as a driver for microbial community dynamics, which may have large impacts on both the local and global marine biogeochemical cycles.

BackgroundThe high invasiveness of phytophagous insects is related to their adaptability to various environments, that can be influenced by their associated microbial community. Microbial symbionts are known to play a key role in the biology, ecology, and evolution of phytophagous insects, but their abundance and diversity are suggested to be influenced by environmental stressors. In this work, using 16 S rRNA metabarcoding we aim to verify (1) if laboratory rearing affects microbial symbiont communities of Zeugodacus cucurbitae females, a cosmopolitan pest of cucurbitaceous crops (2) if temperature, diet quality, and antibiotic treatments affect microbial symbiont communities of both laboratory and wild populations, and (3) if changes in microbial symbiont communities due to temperature, diet and antibiotic affect longevity and fecundity of Z. cucurbitae.ResultsThe results showed that microbial diversity, particularly the β-diversity was significantly affected by insect origin, temperature, diet quality, and antibiotic treatment. The alteration of gut microbial symbionts, specifically Enterobacteriaceae, was associated with low fecundity and longevity of Z. cucurbitae females feeding on optimal diet only. Fecundity reduction in antibiotic treated females was more pronounced when flies were fed on a poor diet without protein.Conclusionsour study proves the relationship between gut microbiome and host fitness under thermal and diet fluctuation highlighting the importance of microbial community in the adaptation of Z. cucurbitae to environmental stress.Clinical trial numberNot applicable.

Deep vertical rotary tillage mitigates salinization hazards and shifts microbial community structure in salt-affected anthropogenic-alluvial soil

Northern peatlands typically develop through succession from fens dominated by the moss family Amblystegiaceae to bogs dominated by the moss genus Sphagnum. How the different plants and abiotic environmental conditions provided in Amblystegiaceae and Sphagnum peat shape the respective moss associated microbial communities is unknown. Through a large-scale molecular and biogeochemical study spanning Arctic, sub-Arctic and temperate regions we assessed how the endo- and epiphytic microbial communities of natural northern peatland mosses relate to peatland type (Sphagnum and Amblystegiaceae), location, moss taxa and abiotic environmental variables. Microbial diversity and community structure were distinctly different between Amblystegiaceae and Sphagnum peatlands, and within each of these two peatland types moss taxon explained the largest part of microbial community variation. Sphagnum and Amblystegiaceae shared few (< 1% of all operational taxonomic units (OTUs)) but strikingly abundant (up to 65% of relative abundance) OTUs. This core community overlapped by one third with the Sphagnum-specific core-community. Thus, the most abundant microorganisms in Sphagnum that are also found in all the Sphagnum plants studied, are the same OTUs as those few shared with Amblystegiaceae. Finally, we could confirm that these highly abundant OTUs were endophytes in Sphagnum, but epiphytes on Amblystegiaceae. We conclude that moss taxa and abiotic environmental variables associate with particular microbial communities. While moss taxon was the most influential parameter, hydrology, pH and temperature also had significant effects on the microbial communities. A small though highly abundant core community is shared between Sphagnum and Amblystegiaceae.

Soil microorganisms interact with one another within soil pores and respond to external conditions such as temperature. Data on microbial community composition and potential function are commonly generated in studies of soils. However, these data do not provide direct insight into the drivers of community composition and can be difficult to interpret outside the context of ecological theory. In this study, we explore the effect of abiotic environmental variation on microbial species diversity. Using a modified version of the Lotka-Volterra Competition Model with temperature-dependent growth rates, we show that environmentally relevant temperature variability may expand the set of temperature-tolerance phenotype pairs that can coexist as two-species communities compared to constant temperatures. These results highlight a potential role of temperature variation in influencing microbial diversity. This in turn suggests a need to incorporate temperature into predictive models of microbial communities in soil and other environments. We recommend future work to parameterize the model applied in this study with empirical data from environments of interest, and to validate the model predictions using field observations and experimental manipulations.

Sponges are ancient metazoans that host diverse and complex microbial communities. Sponge-associated microbial diversity has been studied from wide oceans across the globe, particularly in subtidal regions, but the microbial communities from intertidal sponges have remained mostly unexplored. Here we used pyrosequencing to characterize the microbial communities in 12 different co-occurring intertidal marine sponge species sampled from the Atlantic coast, revealing a total of 686 operational taxonomic units (OTUs) at 97% sequence similarity. Taxonomic assignment of 16S ribosomal RNA tag sequences estimated altogether 26 microbial groups, represented by bacterial (75.5%) and archaeal (22%) domains. Proteobacteria (43.4%) and Crenarchaeota (20.6%) were the most dominant microbial groups detected in all the 12 marine sponge species and ambient seawater. The Crenarchaeota microbes detected in three Atlantic Ocean sponges had a close similarity with Crenarchaeota from geographically separated subtidal Red Sea sponges. Our study showed that most of the microbial communities observed in sponges (73%) were also found in the surrounding ambient seawater suggesting possible environmental acquisition and/or horizontal transfer of microbes. Beyond the microbial diversity and community structure assessments (NMDS, ADONIS, ANOSIM), we explored the interactions between the microbial communities coexisting in sponges using the checkerboard score (C-score). Analyses of the microbial association pattern (co-occurrence) among intertidal sympatric sponges revealed the random association of microbes, favoring the hypothesis that the sponge-inhabiting microbes are recruited from the habitat mostly by chance or influenced by environmental factors to benefit the hosts.

Background. High plant diversity is known to increase carbon inputs to soils, impact soil microbial community composition and promote soil microbial activity. Large pores are likely to hold more roots residues, provide more efficient oxygen supply, and have more dissolved nutrients and carbon carried by water fluxes. Soil pore structure also impacts the activities of soil microbial communities. The aim of this study was to investigate the effects of 1) plant systems, representing a 9-year gradient of plant diversity (no plants, monoculture switchgrass (Panicum virgatum L.), and high diversity prairie), 2) soil pore size (small (4-10 &amp;#181;m &amp;#216;) and large (30-150 &amp;#181;m &amp;#216;)), and 3) incubation time (24 hr (short-term) and 30 days (long-term)) on the microbial communities involved in the utilization of a newly added carbon (glucose). This is the first work to explore the influence of soil micro-habitat, as presented by pores of different sizes ranges, on the microbial communities&amp;#8217; responses to new carbon inputs.Methods. The intact soil cores (5 cm &amp;#216;) from the three systems were supplied with either 50 &amp;#956;M C g-1 soil of&amp;#160;13C labeled glucose, unlabeled glucose, or no glucose. Glucose was added to small or large pores based on matrix potential approach. After 24 hr or 30 day incubations stable isotope probing (SIP) was used to identify the phylotypes actively responsible for glucose assimilation in the small and large pore micro-habitats. Both extracted DNA and the fractions separated by SIP were subject to 16S rRNA gene sequencing. PICRUST2 was used to predict the microbial functions of the sequencing data from KEGG orthologs.Results. The overall microbial communities were affected by multiple years of contrasting vegetation, but not by pore sizes or incubation times. Pseudomonas (Proteobacteria) played an important role in carbon uptake from glucose in all short-term incubations and in the long-term incubations within large pores. In the long-term incubations of both switchgrass and prairie systems&amp;#8217; soils, the community compositions of carbon consumers acting within the small and large pore micro-habitats differed and could be linked to disparate carbon assimilation strategies (r- vs. K-strategists) and to disparate carbon acquisition ecological strategies (plant polymer decomposers, microbial necromass decomposers, predators, and passive consumers). The predicted enriched functional genes indicated the dominance of glucokinase in the soil of the prairie, but not switchgrass system, suggesting a competitive advantage for consuming glucose.

Effective population size (N(e)) is a critical index of the evolutionary capacity of populations. Low N(e) indicates that standing genetic diversity is susceptible to loss via stochastic processes (and inbreeding) and is, therefore, unavailable for natural selection to act upon. Reported N(e) in plant populations is often quite low. What biological and ecological factors might produce such low N(e) • We conducted a simulation model to test the effect of randomly assigned and autocorrelated growth rates of annual plants on plant-size distributions at the end of the growing season. Because plant size is directly correlated with reproductive output in annual plants, variation in plant size reflects variation in reproduction, and thus our modeled size distributions can be used to estimate N(e). • Randomly assigned growth rates had a negligble effect on N(e)/N. Autocorrelated growth rates decreased N(e)/N as the length of the growing season increased. This was the case even when the variance in growth rates was as low as 0.1% of the mean. • While intrinsic plant biology can affect the degree of growth autocorrelation, ecological factors such as competition, herbivory, and abiotic stress can increase or decrease levels of growth autocorrelation. Ecological factors that increase growth autocorrelation can have significant effects on genetic drift within populations.