Maintenance Of Microbial Diversity Research Articles

Decreased spatial variation and deterministic processes of bacterial community assembly in the rhizosphere of Phragmites australis across the Middle-Lower Yangtze plain.

Comparison of the spatial distribution and assembly processes between bulk and rhizosphere bacterial communities at multiple spatial scales is vital for understanding the generation and maintenance of microbial diversity under the influence of plants. However, biogeographical patterns and the underlying mechanisms of microbial communities in bulk and rhizosphere sediments of aquatic ecosystems remain unclear. Here, we collected 140 bulk and rhizosphere sediment samples of Phragmites australis from 14lakeshore zones across a 510-km transect in the Middle-Lower Yangtze plain. We performed high-throughput sequencing to investigate the bacterial diversity, composition, spatial distribution and assembly processes of these samples. Bacterial communities in the rhizosphere sediment exhibited higher alpha diversity but lower beta diversity than those in the bulk sediment. Both bulk and rhizosphere sediment bacterial communities had significant distance-decay relationships, but spatial turnover of the rhizosphere sediment bacterial community was strikingly lower than that of bulk sediment. Despite variable selection dominating the assembly processes of bacterial communities in bulk sediment, the rhizosphere of P. australis enhanced the role of dispersal limitation in governing bacterial communities. The relative importance of different ecological processes in determining bacterial assembly presented distinct patterns of increasing or decreasing linearly with an increase of scale. This investigation highlights the convergent selection of the aquatic plant rhizosphere for surrounding bacterial communities and emphasizes the importance of different ecological processes on bacterial community assembly in sediment environments over different scales. Furthermore, we provide a preliminary framework for exploring the scale dependence of microbial community assembly in aquatic ecosystems.

Bridging Rare and Abundant Bacteria with Ecosystem Multifunctionality in Salinized Agricultural Soils: from Community Diversity to Environmental Adaptation.

ABSTRACTBacterial diversity and ecosystem multifunctionality (EMF) vary along environmental gradients. However, little is known about interconnections between EMF and taxonomic and phylogenetic diversities of rare and abundant bacteria. Using MiSeq sequencing and multiple statistical analyses, we evaluated the maintenance of taxonomic and phylogenetic diversities of rare and abundant bacteria and their contributions to EMF in salinized agricultural soils (0.09 to 19.91 dS/m). Rare bacteria exhibited closer phylogenetic clustering and broader environmental breadths than abundant ones, while abundant bacteria showed higher functional redundancies and stronger phylogenetic signals of ecological preferences than rare ones. Variable selection (86.7%) dominated rare bacterial community assembly, and dispersal limitation (54.7%) and variable selection (24.5%) determined abundant bacterial community assembly. Salinity played a decisive role in mediating the balance between stochastic and deterministic processes and showed significant effects on functions and diversities of both rare and abundant bacteria. Rare bacterial taxonomic α-diversity and abundant bacterial phylogenetic α-diversity contributed significantly to EMF, while abundant bacterial taxonomic α-diversity and rare bacterial phylogenetic α-diversity did not. Additionally, abundant rather than rare bacterial community function had a significant effect on soil EMF. These findings extend our knowledge of environmental adaptation of rare and abundant bacteria and highlight different contributions of taxonomic and phylogenetic α-diversities of rare and abundant bacteria to soil EMF.IMPORTANCE Soil salinization is a worldwide environmental problem and threatens plant productivity and microbial diversity. Understanding the generation and maintenance of microbial diversity is essential to estimate soil tillage potential via investigating ecosystem multifunctionality. Our sequence-based data showed differences in environmental adaptations of rare and abundant bacteria at taxonomic and phylogenetic levels, which led to different contributions of taxonomic and phylogenetic α-diversities of rare and abundant bacteria to soil EMF. Studying the diversity of rare and abundant bacteria and their contributions to EMF in salinized soils is critical for guiding soil restoration.

Environmental adaptation is stronger for abundant rather than rare microorganisms in wetland soils from the Qinghai-Tibet Plateau.

Disentangling the biogeographic patterns of rare and abundant microbes is essential in order to understand the generation and maintenance of microbial diversity with respect to the functions they provide. However, little is known about ecological assembly processes and environmental adaptation of rare and abundant microbes across large spatial-scale wetlands. Using Illumina sequencing and multiple statistical analyses, we characterized the taxonomic and phylogenetic diversity of rare and abundant bacteria and fungi in Qinghai-Tibet Plateau wetland soils. Abundant microbial taxa exhibited broader environmental thresholds and stronger phylogenetic signals for ecological traits than rare ones. By contrast, rare taxa showed higher sensitivity to environmental changes and closer phylogenetic clustering than abundant ones. The null model analysis revealed that dispersal limitation belonging to stochastic process dominated community assemblies of abundant bacteria, and rare and abundant fungi, while variable selection belonging to deterministic process governed community assembly of rare bacteria. Neutral model analysis and variation partitioning analysis further confirmed that abundant microbes were less environmentally constrained. Soil ammonia nitrogen was the crucial factor in mediating the balance between stochasticity and determinism of both rare and abundant microbes. Abundant microbes may have better environmental adaptation potential and are less dispersed by environmental changes than rare ones. Our findings extend knowledge of the adaptation of rare and abundant microbes to ongoing environmental change and could facilitate prediction of biodiversity loss caused probably by climate change and human activity in the Qinghai-Tibet Plateau wetlands.

Metagenomics Reveals That Intravenous Injection of Beta-Hydroxybutyric Acid (BHBA) Disturbs the Nasopharynx Microflora and Increases the Risk of Respiratory Diseases.

It is widely accepted that maintenance of microbial diversity is essential for the health of the respiratory tract; however, there are limited reports on the correlation between starvation and respiratory tract microbial diversity. In the present study, saline/β-hydroxybutyric acid (BHBA) intravenous injection after dietary restriction was used to imitate different degrees of starvation. A total of 13 healthy male yaks were imposed to different dietary restrictions and intravenous injections, and their nasopharyngeal microbiota profiles were obtained by metagenomic shotgun sequencing. In healthy yaks, the main dominant phyla were Proteobacteria (33.0%), Firmicutes (22.6%), Bacteroidetes (17.2%), and Actinobacteria (13.2%); the most dominated species was Clostridium botulinum (10.8%). It was found that 9 days of dietary restriction and 2 days of BHBA injection (imitating severe starvation) significantly decreased the microbial diversity and disturbed its structure and functional composition, which increased the risk of respiratory diseases. This study also implied that oral bacteria played an important role in maintaining nasopharynx microbial homeostasis. In this study, the correlation between starvation and nasopharynx microbial diversity and its potential mechanism was investigated for the first time, providing new ideas for the prevention of respiratory diseases.

Contrasting patterns and drivers of soil bacterial and fungal diversity across a mountain gradient.

Microbial elevational diversity patterns have been extensively studied, but their shaping mechanisms remain to be explored. Here, we examined soil bacterial and fungal diversity and community compositions across a 3.4 km elevational gradient (consists of five elevations) on Mt. Kilimanjaro located in East Africa. Bacteria and fungi had different diversity patterns across this extensive mountain gradient-bacterial diversity had a U shaped pattern while fungal diversity monotonically decreased. Random forest analysis revealed that pH (12.61% importance) was the most important factor affecting bacterial diversity, whereas mean annual temperature (9.84% importance) had the largest impact on fungal diversity, which was consistent with results obtained from mixed-effects model. Meanwhile, the diversity patterns and drivers of those diversity patterns differ among taxonomic groups (phyla/classes) within bacterial or fungal communities. Taken together, our study demonstrated that bacterial and fungal diversity and community composition responded differently to climate and edaphic properties along an extensive mountain gradient, and suggests that the elevational diversity patterns across microbial groups are determined by distinct environmental variables. These findings enhanced our understanding of the formation and maintenance of microbial diversity along elevation, as well as microbial responses to climate change in montane ecosystems.

Divergent patterns of microbial community composition shift under two fertilization regimes revealed by responding species

Using patterns of belowground biodiversity to predict ecological functions and to manage productivity has been a longstanding objective for agronomists and ecologists. However, inconsistent associations between microbial diversity and fertilization have been found in frequency, which can be partly due to the dilution effect of immense silent species in microbial communities. Therefore, we studied the responding pool of the microbial communities, which was determined by filtering out taxa that did not vary significantly between fertilization treatments and the control. With responding species, we hypothesized that the difference of microbial response to different fertilization regimes and between bacterial and fungal response to treatments can be enlarged. In this study, bacterial and fungal community compositions and networks were characterized from soils with chemical fertilization (F), the combined application of chemical fertilizers and organic residues (MRF) and without fertilization (Control) in a 7-year experiment located at the Fengqiu Agroecological Experimental Station. As a result, >90% of the phyla, 75% of the genera and 92% of the OTUs were silent microbes. When filtering out these species, 9 phyla, 88 genera and 185 OTUs of bacteria responded significantly to the MRF treatment compared with those of the Control with an average abundance variation of 0.06% in responding OTUs. In contrast, only 2 phyla, 9 genera and 30 OTUs of bacteria significantly responded to the F treatment with an average amplitude of 0.11%. The higher connectedness and the lower average geodesic distance under the MRF treatment showed a more connective and closer bacterial network compared with the F treatment. Similar but stronger responses were detected in the fungal community composition and networks. To conclude, combined fertilization exerted a moderate impact on many microbial taxa (MM pattern), and chemical fertilization showed a substantial effect on a small amount of taxa (SS pattern). It was further inferred that a variation of the “MM” pattern can result in a more stable, harmonious and efficient ecosystem via maintenance of microbial diversity, stimulation of beneficial species, and exhibition of a more efficient microbial network. Our study showed explicit patterns of microbial communities under fertilization regimes revealed by responding species and highlighted the advantages of combined fertilization with organic matter in agroecosystems.

The ecology of heterogeneity: soil bacterial communities and C dynamics.

Heterogeneity is a fundamental property of soil that is often overlooked in microbial ecology. Although it is generally accepted that the heterogeneity of soil underpins the emergence and maintenance of microbial diversity, the profound and far-reaching consequences that heterogeneity can have on many aspects of microbial ecology and activity have yet to be fully apprehended and have not been fully integrated into our understanding of microbial functioning. In this contribution we first discuss how the heterogeneity of the soil microbial environment, and the consequent uncertainty associated with acquiring resources, may have affected how microbial metabolism, motility and interactions evolved and, ultimately, the overall microbial activity that is represented in ecosystem models, such as heterotrophic decomposition or respiration. We then present an analysis of predicted metabolic pathways for soil bacteria, obtained from the MetaCyc pathway/genome database collection (https://metacyc.org/). The analysis suggests that while there is a relationship between phylogenic affiliation and the catabolic range of soil bacterial taxa, there does not appear to be a trade-off between the 16S rRNA gene copy number, taken as a proxy of potential growth rate, of bacterial strains and the range of substrates that can be used. Finally, we present a simple, spatially explicit model that can be used to understand how the interactions between decomposers and environmental heterogeneity affect the bacterial decomposition of organic matter, suggesting that environmental heterogeneity might have important consequences on the variability of this process. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Long term effects of management practice intensification on soil microbial community structure and co-occurrence network in a non-timber plantation

Intensive forest plantation management practices, such as use of inorganic chemical fertilizer and herbicides improve productivity, however, their environmental impacts on plantation soil microbial communities and its interaction pattern remain unclear. In this study, we investigated associations between management practice intensities (nutrient-herbicide, nutrient-mowing and manure-mowing), environmental factors including plant coverage, pH, exchangeable calcium (Ca2+), aluminium ion (Al3+), total organic carbon (TOC), C to N ratio (C/N) and soil moisture (SM), and microbial community structure in Chinese hickory (Carya cathayenses) plantations cultivated on two soil types (calcareous and yellow soils). Our results demonstrated that long-term management practices with different intensities significantly changed certain soil environmental factors, and revealed a significant impact on both α and β-diversity of soil bacterial and fungal communities. Specifically, significant higher values of plant coverage, pH, Ca2+, TOC, C/N and SM and lower value of Al3+ were observed under manure-mowing management. Calcareous soil showed significantly higher pH, Ca2+ and TN contents and lower AP values than yellow soil across all three operating intensities. The bacterial community structure was different between the calcareous and yellow soil, but there was no difference for the fungi. Edaphic properties such as pH, Ca2+, TOC and TN were shown to play crucial roles in microbial community structuring, while vegetation-associated factors (vegetation coverage and Al3+) were correlated with fungal community structure. The complexity of microbe co-occurrence network decreased as management practice intensified. The keystone taxa including Bradyrhizobium, Reyranella and Phaselicystis in bacterial network and Rhizophydium and Microascales in fungal network were only observed under manure-mowing, with ecological functions mainly involved in organic carbon degradation and nitrogen fixation. Our results provide insight into the interactions between management practice intensities and soil microbial community characteristics and have implications for the optimization of sustainable forestry management practices and maintenance of microbial diversity and network complexity in over-managed forest plantations.

The Gut Microbiota in Causation, Detection, and Treatment of Cancer.

The gut microbiota has emerged as an important consideration in clinical oncology. The role of the microbiome in cancer extends beyond causation and cancer risk. It is now known that the microbiome not only acts at a local epithelial level in the gut but also modifies immune responses within intestinal and extraintestinal tumors. Microbial signaling influences the clinical course of cancer including the efficacy, bioavailability, and toxicity of chemotherapeutic and immunotherapy agents. This has focused research on microbiota profiling in different cancer states with an aim of developing prognostic biomarkers of risk. The potential value of microbiome manipulation with live biotherapeutics or microbial transplantation has also become a realistic consideration. Maintenance of microbial diversity in patients with cancer is a variable challenge given the modifying influences of the tumor itself, chemotherapy, nutritional status, and sporadic antimicrobial therapy. Here, we address current evidence for the role of the microbiome in cancer therapy.

Dispersal alters bacterial diversity and composition in a natural community.

Dispersal is central to the evolution and maintenance of microbial diversity. Quantifying microbial dispersal and its role in shaping communities remains a challenge, however. Here, we manipulated a bacterial community's dispersal rate in a grassland ecosystem and test whether this altered diversity and composition. We constructed bags of two nylon mesh sizes that allowed more or less bacterial movement and filled them with an edible or inedible substrate, irradiated plant litter or nylon sheets. We measured changes in bacterial abundance (using flow cytometry) and composition (using 16S amplicon sequencing) in the bags weekly over 5 months. The dispersal treatment altered bacterial colonization rates and led to differences in the abundance, richness, evenness and composition of communities. Overall, the study demonstrates that dispersal influences the assembly of this natural bacterial community.

History Leaves Its Mark on Soil Bacterial Diversity.

ABSTRACTDispersal 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.

Exometabolite niche partitioning among sympatric soil bacteria.

Soils are arguably the most microbially diverse ecosystems. Physicochemical properties have been associated with the maintenance of this diversity. Yet, the role of microbial substrate specialization is largely unexplored since substrate utilization studies have focused on simple substrates, not the complex mixtures representative of the soil environment. Here we examine the exometabolite composition of desert biological soil crusts (biocrusts) and the substrate preferences of seven biocrust isolates. The biocrust's main primary producer releases a diverse array of metabolites, and isolates of physically associated taxa use unique subsets of the complex metabolite pool. Individual isolates use only 13−26% of available metabolites, with only 2 out of 470 used by all and 40% not used by any. An extension of this approach to a mesophilic soil environment also reveals high levels of microbial substrate specialization. These results suggest that exometabolite niche partitioning may be an important factor in the maintenance of microbial diversity.

Resolving the abundance and air-sea fluxes of airborne microorganisms in the North Atlantic Ocean.

Airborne transport of microbes may play a central role in microbial dispersal, the maintenance of diversity in aquatic systems and in meteorological processes such as cloud formation. Yet, there is almost no information about the abundance and fate of microbes over the oceans, which cover >70% of the Earth's surface and are the likely source and final destination of a large fraction of airborne microbes. We measured the abundance of microbes in the lower atmosphere over a transect covering 17° of latitude in the North Atlantic Ocean and derived estimates of air-sea exchange of microorganisms from meteorological data. The estimated load of microorganisms in the atmospheric boundary layer ranged between 6 × 104 and 1.6 × 107 microbes per m2 of ocean, indicating a very dynamic air-sea exchange with millions of microbes leaving and entering the ocean per m2 every day. Our results show that about 10% of the microbes detected in the boundary layer were still airborne 4 days later and that they could travel up to 11,000 km before they entered the ocean again. The size of the microbial pool hovering over the North Atlantic indicates that it could play a central role in the maintenance of microbial diversity in the surface ocean and contribute significantly to atmospheric processes.

Effect of Kampo medicine “Dai-kenchu-to” on microbiome in the intestine of the rats with fast stress

Diversity of gut microbiome has been recently reported to be lost in inflammatory bowel disease. We have previously reported that the Dai-kenchu-to (DKT) prevented the bacterial translocation through suppression of cytokine and apoptosis in rat's fast stress model. The aim of this study was to evaluate the effect of DKT on maintenance of microbial diversity in rat's intestine with inflammation. Wister rats were received the fast stress for 5 days. In DKT group, rats were administered with DKT (300 mg/kg/day) during the fast stress (DKT-group). The gut microbiomes were analyzed at before- and after- fast stress, and the effect of DKT for on microbial diversities of the gut were evaluated by the PCR-clone library method targeting the 16 S ribosomal RNA gene. In Control-group, Erysipelotrichaceae increased to 86% in after fast stress, OTU of before-fast stress was 111 and after fast stress was only 9 (changing rate: 58%). The diversity of microbiome was severely decreased. On the other hand, in DKT-group, diversity of microbiome was kept after fast stress (Lachnospiraceae: Ruminococcaceae: Coriobacteriales 54%, 22%, 5%), Operational taxonomic units of before fast stress was 52 and after fast stress was 55 (changing rate: 6%). Family Lachnospiraceae which includes butyrate-producing Clostridia (Clostridium IV and XIVa). DKT prevented the reduction of diversity of microbiome in rat's fast stress model. Our data suggested the new anti-inflammatory mechanism of DKT through gut microbiome.

A simplified analysis of granule behavior in ASBR and UASB reactors treating low-strength synthetic wastewater

This work presents an analysis of the changes observed in granule characteristics of sludge in the treatment of synthetic wastewater at a concentration of about 500 mgCOD/L in batch, fed-batch (ASBR) and continuous (UASB) bench-scale reactors under similar experimental conditions. Physical and microbiological properties of the granules were characterized as average particle size and sedimentation time and by optical and epifluorescence microscopy. Several samples were analyzed in order to identify the morphologies. Granules from sequencing batch and fed-batch reactors, either with or without mechanical mixing, did not undergo any physical or microbiological changes. However, during the experiment granules from the UASB reactor agglomerated due to the formation and accumulation of a viscous material, probably of microbial origin, when operated at low superficial velocities (0.072, 0.10 and 0.19 m/h). When the superficial velocity was increased to 8.0-10.0 m/h by means of liquid-phase recirculation, the granules from the UASB reactor underwent flocculation and the microbiological characteristics changed in such a way that the equilibrium of microbial diversity in the inoculum was not maintained. As a result, the only reactor that maintained efficiency and good solids retention during the assays was the ASBR, showing that there is a correlation between maintenance of microbial diversity and operating mode in the case of anaerobic treatment of low-strength wastewaters.