Distinct Community Structure Research Articles

Contrasting effects of microbial fertiliser and organic fertiliser on soil bacterial community in coal mine dump of Inner Mongolia

ABSTRACT Knowledge about fertiliser limitation to soil microbes is crucial for exploring microbial community succession and ecosystem functions. In this study, an experiment was conducted to promote ecological restoration by different treatments of organic fertiliser (OF), microbial fertiliser (MF) and non-fertiliser (CK) in a coal mine dump. We investigated microbial community structure using high-throughput sequencing. Soils under OF and MF treatment showed distinct community structures with highly bacterial α-diversity due to the variation of soil pH and organic matters (SOM). Of those, the community dissimilarity between OF and CK was higher. The DistLM analysis indicated that SOM and available nitrogen (AN) significantly influenced microbial community structure. Furthermore, functional annotation by the FAPROTAX revealed that the functional groups associating with C, N, and S cycling increased significantly under OF and MF treatment, but decreased that associated with parasites or symbionts. Compared with MF, the functional groups with OF treatment varied greatly. However, the function groups including nitrogen_fixation, hydrocarbon_degradation and methanotrophy were significantly improved under the MF treatment, which have an important implication for soil quality and microbial growth. It was concluded that MF treatment could improve microbial community structure and enhance potential ecosystem function in coal mine dump soils.

Distribution of phytoplankton in Pangkep Waters, South Sulawesi, Indonesia

The coastal water of Pangkajene Kepulauan, or Pangkep, in South Sulawesi has been influenced by high anthropogenic activities, where the inflow of nutrient from the land has caused several cases of harmful algal blooms and mass fish mortality. Thus, it was important to understand the community structure and distribution of phytoplankton, with particular interest on the bloom-forming and harmful genus, to better mitigate the effects of harmful algal blooms in the future. Sample collection for this study was conducted on May 2017 at 22 stations from three zones, the northern, middle, and southern coastal area of Pangkep. From this study, the phytoplankton density in Pangkep was found varied between 2.179 × 106 cells/m3 to 2.192 × 108 cells/m3, with the highest density of phytoplankton was observed in the northern and southern area of Pangkep. On the other hand, the middle area has lower phytoplankton density but has the highest diversity and evenness. Two stations, station 15 and 21, have a distinct phytoplankton community structure which might have caused by a combined effect of temperature and nutrient input from the land. Twenty-nine genera of phytoplankton were observed, with the diatoms Skeletonema as the most dominant genus which contributes to over 95% of total phytoplankton density. The occurrence of Ceratium, which once was found as a dominant genus in Pangkep coastal and estuaries, has caused a concern whether it might blooms and replacing the dominance of diatoms in these areas.

Soil Mesofauna Community Changes in Response to the Environmental Gradients of Urbanization in Guangzhou City

There has been a recent increase in interest on how urbanization affects soil fauna communities. However, previous studies primarily focused on some limited land use types or line transects of urban-rural gradients. At family and higher taxonomic levels, we investigated the changes of soil mesofauna communities (abundance, species richness, and community structure) with urbanization intensity along different disturbance features in 47 sites evenly located in downtown Guangzhou and adjacent regions. The 47 research sites were classified into four ecosystem types mainly according to the location (rural/urban), vegetation cover, and management intensity. In turn, the four types with increasing urbanization intensity were rural forest, urban forest, urban woodland, and urban park. Firstly, the role of urban soil property (soil physicochemical characteristic and soil heavy metal content) in regulating soil mesofauna community was investigated. The results showed that soil mesofauna abundance and diversity decreased with increasing soil pH, total nitrogen content (TN), and heavy metal comprehensive index (CPI). Soil Pb decreased soil mesofauna species richness (taxa number) and regulated soil mesofauna community structure. Secondly, we examined the effects of landscape changes on the soil mesofauna community. We found impervious surface (IS) ratio did not predict changes in soil mesofauna abundance, species richness, or community structure. Instead, IS ratio was positively correlated with soil pH, soil TN, and CPI. After excluding sites that belonged to rural forests and urban parks, site area was positively correlated with soil mesofauna abundance. Thirdly, our results revealed significant differences in soil property, landscape trait, and soil mesofauna community among the four ecosystem types. Interestingly, urban forest, the one lightly disturbed by urbanization, but not rural forest, had the highest soil mesofauna abundance. Soil mesofauna abundance in urban woodlands was similar to that in urban parks, which was about half of that in urban forests. Species richness in urban parks was 21% lower than that in rural forests. Our results also showed that urban woodland and urban parks had distinct mesofauna community structures compared to those in rural forests and urban forests. In conclusion, the present study suggested that (1) soil property changes due to urbanization, such as increased pH and heavy metal enrichment in urban soil, decreased soil mesofauna abundance and species richness, changed community structure, and mediated the effect of landscape change on soil mesofauna community; (2) however, soil and landscape changes could not explain the increase of abundance in urban forests, which supported the intermediate disturbance hypothesis.

Riparian Vegetation Structure Influences Terrestrial Invertebrate Communities in an Agricultural Landscape

Stream and terrestrial ecosystems are intimately connected by riparian zones that support high biodiversity but are also vulnerable to human impacts. Landscape disturbances, overgrazing, and diffuse pollution of agrochemicals threaten riparian biodiversity and the delivery of ecosystem services in agricultural landscapes. We assessed how terrestrial invertebrate communities respond to changes in riparian vegetation in Romanian agricultural catchments, with a focus on the role of forested riparian buffers. Riparian invertebrates were sampled in 10 paired sites, with each pair consisting of an unbuffered upstream reach and a downstream reach buffered with woody riparian vegetation. Our results revealed distinct invertebrate community structures in the two site types. Out of 33 invertebrate families, 13 were unique to either forested (6) or unbuffered (7) sites. Thomisidae, Clubionidae, Tetragnathidae, Curculionidae, Culicidae, and Cicadidae were associated with forested buffers, while Lycosidae, Chrysomelidae, Staphylinidae, Coccinellidae, Tettigoniidae, Formicidae, and Eutichuridae were more abundant in unbuffered sites. Despite statistically equivocal results, invertebrate diversity was generally higher in forested riparian buffers. Local riparian attributes significantly influenced patterns in invertebrate community composition. Our findings highlight the importance of local woody riparian buffers in maintaining terrestrial invertebrate diversity and their potential contribution as a multifunctional management tool in agricultural landscapes.

Distinct bacterial community structure and composition along different cowpea producing ecoregions in Northeastern Brazil

Soil microbial communities represent the largest biodiversity on Earth, holding an important role in promoting plant growth and productivity. However, the knowledge about how soil factors modulate the bacteria community structure and distribution in tropical regions remain poorly understood, mainly in different cowpea producing ecoregions belonging to Northeastern Brazil. This study addressed the bacterial community along three different ecoregions (Mata, Sertão, and Agreste) through the16S rRNA gene sequencing. The results showed that soil factors, such as Al3+, sand, Na+, cation exchange excel, and total organic C, influenced the bacterial community and could be a predictor of the distinct performance of cowpea production. Also, the bacterial community changed between different ecoregions, and some keystone groups related to plant-growth promotion, such as Bradyrhizobium, Bacillales, Rhizobiales, and Solibacillus, were correlated to cowpea yield, so revealing that the soil microbiome has a primordial role in plant productivity. Here, we provide evidence that bacterial groups related to nutrient cycling can help us to increase cowpea efficiency and we suggest that a better microbiome knowledge can contribute to improving the agricultural performance.

Distinct taxonomic composition of soil bacterial community across a native gradient of Cerrado-Ecotone-Caatinga

Biodiversity underlies ecosystem functioning, and the soil microbiome plays a crucial role in these functional processes. A better understanding of the soil microbiome and the relationship between microbial diversity and environmental parameters would increase our ability to set conservation priorities. In recent years, ecotones have been considered an important issue in ecological studies since they are ecosystems located in the transition between two biomes where communities meet and integrate. Here, we hypothesized that each area of the environmental gradient Cerrado-Ecotone-Caatinga would harbor a distinct bacterial community mainly shaped by the differential environmental factors. To test this hypothesis, the bacterial community was assessed using the 16S rRNA gene sequencing and correlated with environmental parameters. Our analysis revealed that each area presented a distinct community structure and composition that was related to changes in environmental parameters such as pH, Al, and temperature. Although we did not find significant differences in the microbial diversity, the network analysis showed a gradient with a decreased complexity from the Cerrado to Caatinga also as a response of the soil characteristics, with changes in the number of correlations and the proportion of co-occurrence and competition. Also, the compositional analysis revealed that the most abundant bacterial group in each area is related to functional adaptation to soil properties. Overall, our findings expand our knowledge about the microbiome of these areas and add important information that can be suitable for future ecosystem exploration and the development of preservation strategies.

Plant Age Influences Microbiome Communities More Than Plant Compartment in Greenhouse-Grown Creeping Bentgrass

Creeping bentgrass (Agrostis stolonifera) is widely used in golf course settings for its desirable playing surface characteristics; however, it is highly susceptible to diseases that can disrupt surface integrity and cause significant losses despite preventative management. Understanding the influence of early plant growth and basic management practices on microbiome communities are crucial first steps to developing future efforts to harness the microbiome for plant health. This study investigated bacterial and fungal communities of creeping bentgrass foliage and rhizosphere through 6 months postemergence under a controlled environment to elucidate microbiome community dynamics in response to plant age. We hypothesized that plant compartments will host distinct community structures and exhibit different responses to plant age. Our results showed that predominant bacterial phyla and fungal classes remain consistent across time and plant compartment. However, genus-level classification revealed that bacterial taxa differed across plant compartment while fungal taxa remained consistent. Host influence over the microbiome manifests quickly, with the largest shift in both microbial communities occurring between emergence and 2 months postemergence. For example, Burkholderia and Penicillium spp. were present at high relative abundance at emergence but, by 2 months postemergence, both taxa decreased significantly. Bacterial communities continued to experience significant fluctuation in rare taxa from 2 months postemergence onward, while fungal community structure was driven by the fluctuation of the most common taxa. These results highlight the connection between plant age and microbial community structure in creeping bentgrass in addition to underscoring future research efforts in creeping bentgrass microbiome manipulation for plant health. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Root-associated (rhizosphere and endosphere) microbiomes of the Miscanthus sinensis and their response to the heavy metal contamination

The plant root-associated microbiomes, including both the rhizosphere and the root endosphere microbial community, are considered as a critical extension of the plant genome. Comparing to the well-studied rhizosphere microbiome, the understanding of the root endophytic microbiome is still in its infancy. Miscanthus sinensis is a pioneering plant that could thrive on metal contaminated lands and holds the potential for phytoremediation applications. Characterizing its root-associated microbiome, especially the root endophytic microbiome, could provide pivotal knowledge for phytoremediation of mine tailings. In the current study, M. sinensis residing in two Pb/Zn tailings and one uncontaminated site were collected. The results demonstrated that the metal contaminant fractions exposed strong impacts on the microbial community structures. Their influences on the microbial community, however, gradually decreases from the bulk soil through the rhizosphere soil and finally to the endosphere, which resulting in distinct root endophytic microbial community structures compared to both the bulk and rhizosphere soil. Diverse members affiliated with the order Rhizobiales was identified as the core microbiome residing in the root of M. sinensis. In addition, enrichment of plant-growth promoting functions within the root endosphere were predicted, suggesting the root endophytes may provide critical services to the host plant. The current study provides new insights into taxonomy and potential functions of the root-associated microbiomes of the pioneer plant, M. sinensis, which may facilitate future phytoremediation practices.

Comparative Gut Microbiome Differences between Ferric Citrate and Calcium Carbonate Phosphate Binders in Patients with End-Stage Kidney Disease.

Gut dysbiosis in patients with chronic kidney disease (CKD) may induce chronic inflammation and increase morbidity. Phosphate-binding agents, generally used in patients with CKD, may potentially change the composition of the gut microbiota. This study aimed to compare the microbiota composition in hemodialysis patients treated with ferric citrate or calcium carbonate. The stool microbiota was investigated in hemodialysis patients treated with ferric citrate (n = 8) and calcium carbonate (n = 46) using 16S rRNA gene amplicon sequencing profiling using linear discriminant analysis of effect size. Further predictive functional profiling of microbial communities was obtained with Tax4Fun in R. Hemodialysis patients treated with calcium carbonate had a significantly reduced microbial species diversity (Shannon index and Simpson index) and an increased microbial alteration ratio compared with patients treated with ferric citrate. A distinct microbial community structure was found in patients treated with ferric citrate, with an increased abundance of the Bacteroidetes phylum and a decreased abundance of the phylum Firmicutes. Members of the order Lactobacillales were enriched in patients treated with calcium carbonate, whereas taxa of the genera Ruminococcaceae UCG-004, Flavonifractor, and Cronobacter were enriched in patients treated with ferric citrate phosphate binder. In conclusion, Ferric citrate therapy results in a more diverse microbiome community compared to calcium carbonate therapy in hemodialysis patients with phosphate binder treatment. The gut microbiome reflects the phosphate binder choice in hemodialysis patients, further affecting the physiological environment in the gastrointestinal tract.

Seascape Configuration Influences the Community Structure of Marsh Nekton

Around the globe, salt marsh ecosystems are rapidly changing, leading to alterations in both the amount, and configuration of marsh habitats. Sea level rise is a key driver of salt marsh change and is decreasing marsh habitat cover while increasing fragmentation. Such changes in seascape structure are expected to alter the ecological communities associated with marsh habitats. The influence of seascape structure on marsh nekton community structure is not well characterized, especially in coastal areas of the Gulf of Mexico, such as Louisiana (USA). Louisiana is losing marsh habitat at an unprecedented rate, and the resulting habitat loss and fragmentation provides a unique study system to investigate how marsh seascape structure impacts the nekton community. In this study, seascape structure was characterized at the 1- and 5-km scale at sampling points across several coastal basins to test marsh seascape structure effects on nekton community characteristics. Nekton communities were sampled using seine nets across coastal Louisiana in 2007. Total nekton community structure was found to be spatially driven. Both nekton species richness and nekton abundance were influenced by the shape of marsh patches and proportion of landscape marsh measured at either scale. While species richness differed only between some of the basins, each basin was found to have a statistically distinct community structure. Marsh shape influenced brown and white shrimp size. However, the response direction was found to be species specific, with brown shrimp size increasing in marshes with more complex shape while white shrimp size decreased. This study demonstrates that both environmental drivers and seascape structure play important roles in structuring marsh nekton communities, and that these responses can be species-specific. In order to project complex interactions between coastal land loss and their communities, a holistic framework of community structure, environmental drivers, and seascape characteristics is recommended.

Distinct Distribution of Archaea From Soil to Freshwater to Estuary: Implications of Archaeal Composition and Function in Different Environments.

In addition to inhabiting extreme territories, Archaea are widely distributed in common environments spanning from terrestrial to aquatic environments. This study investigated and compared archaeal community structures from three different habitats (representing distinct environments): agriculture soils (from farming system trials FST, PA, United States), freshwater biofilms (from White Clay Creek, PA, United States), and estuary water (Chesapeake Bay, United States). High-throughput sequencing of 16S rRNA genes indicated that Thaumarchaeota, Euryarchaeota, Nanoarchaeota, Crenarchaeota, and Diapherotrites were the commonly found dominant phyla across these three environments. Similar to Bacteria, distinct community structure and distribution patterns for Archaea were observed in soils vs. freshwater vs. estuary. However, the abundance, richness, evenness, and diversity of archaeal communities were significantly greater in soils than it was in freshwater and estuarine environments. Indicator species (or amplicon sequence variants, ASVs) were identified from different nitrogen and carbon cycling archaeal groups in soils (Nitrososphaerales, Nitrosotaleales, Nitrosopumilales, Methanomassiliicoccales, Lainarchaeales), freshwater biofilms (Methanobacteria, Nitrososphaerales) and Chesapeake Bay (Marine Group II, Nitrosopumilales), suggesting the habitat-specificity of their biogeochemical contributions to different environments. Distinct functional aspects of Archaea were also confirmed by functional predictions (PICRUSt2 analysis). Further, co-occurrence network analysis indicated that only soil Archaea formed stable modules. Keystone species (ASVs) were identified mainly from Methanomassiliicoccales, Nitrososphaerales, Nitrosopumilales. Overall, these results indicate a strong habitat-dependent distribution of Archaea and their functional partitions within the local environments.

A comparison of bacterial communities from OMZ sediments in the Arabian Sea and the Bay of Bengal reveals major differences in nitrogen turnover and carbon recycling potential

ABSTRACT The Northern Indian Ocean hosts two Oxygen Minimum Zones (OMZ), one in the Arabian Sea and the other in the Bay of Bengal. 16S rRNA gene amplicon sequencing was used to understand the total bacterial diversity in, the surface sediment off Goa within the OMZ of the Arabian Sea, and off Paradeep within the OMZ of the Bay of Bengal. Functional profiling was carried out to pinpoint the occurrence of specific bacterial operational taxonomic units (OTUs) which have been previously described to harbour certain genes/enzymes relevant to biogeochemical cycling of carbon, nitrogen, and sulfur compounds. The dominant phyla identified included Firmicutes (33.08%) and Proteobacteria (32.59%) from the Arabian Sea, and Proteobacteria (52.65%) and Planctomycetes (9.36%) from the Bay of Bengal. Only 30% of OTUs were shared between the sites which make up three-fourth of the Bay of Bengal OMZ bacterial community, but only one-fourth of the Arabian Sea OMZ sediment bacterial community. Statistical analysis indicated the bacterial diversity from sediments of the Bay of Bengal OMZ is ∼48% higher than the Arabian Sea OMZ. The community analysis combined with a predictive functional profiling of 16S rRNA amplicons revealed some major differences regarding sediment nitrogen fixation and carbon recycling, and identified a distinct bacterial community structure within the two shallow OMZ sites lying in the east coast and west coast of the peninsular India.

The response of the soil bacterial community and function to forest succession caused by forest disease

Abstract Forest succession is a key driver of plant communities and understanding succession is central to forest restoration. Currently, the information on the response of the microbial community to the forest succession process, however, is limited. In the present study, we investigated the dynamics of the soil bacterial community in three forest types undergoing succession caused by pine wilt disease, representing the initial pine forest, gradual mixed pine and broadleaved forest, and eventual broadleaved forest, using Illumina MiSeq coupled with Functional Annotation of Prokaryotic Taxa (FAPROTAX) analysis. The results showed that the soil pH, contents of soil organic carbon (SOC) and soil total nitrogen (TN) increased after the occurrence of initial succession and differed among the forest sites. The mixed pine forest had significantly higher bacteria biomass (p < 0.05), whereas, the total microbial biomass did not differ during the succession. The bacterial community diversity and richness increased significantly following the succession process (p < 0.05). Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes were the dominant phyla across the succession, in which the abundance of Bacteroidetes significantly increased (p < 0.05), whereas, Planctomycetes, WPS‐2 and Burkholder decreased in abundance after succession occurred (p < 0.05). The three forests formed distinct bacterial community structures during the succession (p < 0.05), whereas, only two functional structures were clustered, in which the mixed and pure broadleaved forest did not differ. The dominant functional groups involved in the C cycle in the initial pure pine forest were replaced gradually by the groups involved in N and S cycles following the subsequent succession. The soil pH, soil TN and SOC were the most important factors affecting the bacterial community and functional structures during the succession. These results indicate that the bacterial community and function shift drastically in the early stages of succession, which reflects the changes in ecological environment caused by succession. The findings provide useful information to better understand the response of microbes to natural forest disturbance and highlight the importance of microbes during forest succession. A free Plain Language Summary can be found within the Supporting Information of this article.

Methane production in harmful algal blooms collapsed water: The contribution of non-toxic Microcystis aeruginosa outweighs that of the toxic variety

Cyanobacterial blooms can promote CH4 production. The proportions of toxic and non-toxic Microcystis aeruginosa spatiotemporally vary in algal water. However, the comparative contributions of decomposed toxic and non-toxic M. aeruginosa to methane (CH4) production are poorly understood. Here, a 61-day microcosm study was conducted to simulate the collapse processes of toxic and non-toxic M. aeruginosa. The results illustrated that the decomposition of M. aeruginosa induced anaerobic and nutrient-rich conditions in the water. However, the presence of non-toxic M. aeruginosa promoted the release of protein-like substances and aromatic proteins that are readily utilized by methanogens. In comparison, the release of microcystins by toxic M. aeruginosa resulted in a distinctive microorganism community structure. The relative abundance of dominant methanogens in the sediment of the system containing toxic M. aeruginosa was markedly lower than that of the system containing the non-toxic strain at the end of incubation. Despite the fact that almost equal amounts of total carbon were present in the two systems, the CH4 production per unit particulate total carbon (identified as carbon content vs. algal biomass) in the system containing non-toxic M. aeruginosa was 1.74-fold higher than that in the system containing the toxic strain. Considering these observations, it is likely that the currently predicted CH4 mass in algal waters is inaccurate, and should be considered when estimating CH4 emissions in eutrophic freshwater.

Root-Associated Mycobiome Differentiate between Habitats Supporting Production of Different Truffle Species in Serbian Riparian Forests.

Balkan lowlands bordering with the Pannonia region are inhabited by diverse riparian forests that support production of different truffle species, predominantly the most prized white truffle of Piedmont (Tuber magnatum Pico), but also other commercial species (T. macrosporum Vitt., T. aestivum Vitt.). Surprisingly, little is known about the native root-associated mycobiome (RAM) of these lowland truffle-producing forests. Therefore, in this study we aim at exploring and comparing the RAMs of three different truffle-producing forests from Kolubara river plane in Serbia. Molecular methods based on next generation sequencing (NGS) were used to evaluate the diversity of root-associated fungal communities and to elucidate the influence of environmental factors on their differentiation. To our knowledge, this is the first study from such habitats with a particular focus on comparative analysis of the RAM in different truffle-producing habitats using a high-throughput sequencing approach. Our results indicated that the alpha diversity of investigated fungal communities was not significantly different between different truffle-producing forests and within a specific forest type, while the seasonal differences in the alpha diversity were only observed in the white truffle-producing forests. Taxonomic profiling at phylum level indicated the dominance of fungal OTUs belonging to phylum Ascomycota and Basidiomycota, with very minor presence of other phyla. Distinct community structures of root-associated mycobiomes were observed for white, mixed, and black truffle-producing forests. The core mycobiome analysis indicated a fair share of fungal genera present exclusively in white and black truffle-producing forest, while the core genera of mixed truffle-producing forests were shared with both white and black truffle-producing forests. The majority of detected fungal OTUs in all three forest types were symbiotrophs, with ectomycorrhizal fungi being a dominant functional guild. Apart from assumed vegetation factor, differentiation of fungal communities was driven by factors connected to the distance from the river and exposure to fluvial activities, soil age, structure, and pH. Overall, Pannonian riparian forests appear to host diverse root-associated fungal communities that are strongly shaped by variation in soil conditions.

Seasonal Water Level Fluctuation and Concomitant Change of Nutrients Shift Microeukaryotic Communities in a Shallow Lake

Seasonal water level fluctuations (WLFs) impose dramatic influences on lake ecosystems. The influences of WLFs have been well studied for many lake biotas but the microeukaryotic community remains one of the least-explored features. This study employed high-throughput 18S rRNA gene sequencing to investigate the spatiotemporal patterns of microeukaryotic communities in the dry and wet seasons with concomitant change of nutrients in Poyang Lake, which experiences huge seasonal WLFs. The results showed that the dry season and wet season had distinct microeukaryotic community compositions and structures. In the dry season, Ciliophora (13.86–40.98%) and Cryptomonas (3.69–18.64%) were the dominant taxa, and the relative abundance of these taxa were significant higher in the dry season than wet season. Ochrophyta (6.88–45.67%) and Chlorophyta (6.31–22.10%) was the dominant taxa of microeukaryotic communities in the wet season. The seasonal variation of microeukaryotic communities was strongly correlated to seasonal nutrient variations. Microeukaryotic communities responded significantly to dissolved organic carbon, total nitrogen, nitrate, and soluble reactive phosphorus in the dry season, and correlated to nitrate and total phosphorus in the wet season. The microeukaryotic community showed different modular structures in two seasons, and nutrient variations were the key factors influencing seasonal variations of the modular structures. Moreover, microeukaryotic community networks based on different seasons indicated that the microeukaryotic community co-occurrence patterns were not constant but varied largely associating with the nitrogen and phosphorus variations under the effects of WLFs. Our results are important for understanding how microeukaryotic communities respond to nutrient variation under seasonal water level fluctuation.

The gut mycobiota of rural and urban individuals is shaped by geography

BackgroundUnderstanding the structure and drivers of gut microbiota remains a major ecological endeavour. Recent studies have shown that several factors including diet, lifestyle and geography may substantially shape the human gut microbiota. However, most of these studies have focused on the more abundant bacterial component and comparatively less is known regarding fungi in the human gut. This knowledge deficit is especially true for rural and urban African populations. Therefore, we assessed the structure and drivers of rural and urban gut mycobiota.ResultsOur participants (n = 100) were balanced by geography and sex. The mycobiota of these geographically separated cohorts was characterized using amplicon analysis of the Internal Transcribed Spacer (ITS) gene. We further assessed biomarker species specific to rural and urban cohorts. In addition to phyla which have been shown to be ubiquitous constituents of gut microbiota, Pichia were key constituents of the mycobiota. We found that geographic location was a major driver of gut mycobiota. Other factors such as smoking where also determined gut mycobiota albeit to a lower extent, as explained by the small proportion of total variation. Linear discriminant and the linear discriminant analysis effect size analysis revealed several distinct urban and rural biomarkers.ConclusionsTogether, our analysis reveals distinct community structure in urban and rural South African individuals. Geography was shown to be a key driver of rural and urban gut mycobiota.

Effect of predation on the mechanical properties and detachment of MABR biofilms

The membrane-aerated biofilm reactor (MABR) is an emerging wastewater treatment technology that uses O2-supplying membranes as a biofilm support. Because O2 is supplied from the biofilm base instead of the bulk liquid, MABR biofilms have distinct microbial community structures and behavior. Past research showed that protozoan predation in MABR biofilms can greatly increase biofilm porosity, producing a void layer at the base of the biofilm. We hypothesized that this void layer could weaken the biofilm and promote sloughing, and investigated this with heterotrophic MABR biofilms. A rheometer was used to measure biofilm mechanical strength, and MABR flow cells were used to explore detachment. MABRs supplied with cycloheximide, a protozoan inhibitor, were used as controls. Predation increased the internal void ratio from 6 ± 7% to 50 ± 16%. The storage modulus was 1,780 ± 1,180 Pa with predation condition, compared to 9,800 ± 4,290 Pa for the control. Similarly, the loss modulus was 1,580 ± 729 Pa with predation and 363 ± 189 Pa for the control. When subjected to an increased flow, the biofilm loss was 44 ± 24% for the flow cell with predation, while only 7 ± 9% for the control. This research shows that predation can have an important impact on biofilm porosity in MABRs, reducing the mechanical strength and increasing detachment. Understanding this phenomenon can help develop more effective biofilm control strategies in MABRs.

Alteration of Bacterial Wilt Resistance in Tomato Plant by Microbiota Transplant.

Plant-associated microbiota plays an important role in plant disease resistance. Bacterial wilt resistance of tomato is a function of the quantitative trait of tomato plants; however, the mechanism underlying quantitative resistance is unexplored. In this study, we hypothesized that rhizosphere microbiota affects the resistance of tomato plants against soil-borne bacterial wilt caused by Ralstonia solanacearum. This hypothesis was tested using a tomato cultivar grown in a defined soil with various microbiota transplants. The bacterial wilt-resistant Hawaii 7996 tomato cultivar exhibited marked suppression and induction of disease severity after treatment with upland soil-derived and forest soil-derived microbiotas, respectively, whereas the transplants did not affect the disease severity in the susceptible tomato cultivar Moneymaker. The differential resistance of Hawaii 7996 to bacterial wilt was abolished by diluted or heat-killed microbiota transplantation. Microbial community analysis revealed the transplant-specific distinct community structure in the tomato rhizosphere and the significant enrichment of specific microbial operational taxonomic units (OTUs) in the rhizosphere of the upland soil microbiota-treated Hawaii 7996. These results suggest that the specific transplanted microbiota alters the bacterial wilt resistance in the resistant cultivar potentially through a priority effect.

Microbial carbon metabolic functions of biofilms on plastic debris influenced by the substrate types and environmental factors

As an artificial type of microbial carrier, plastic debris has been widely detected in freshwater habitats, and the potential impacts of the plastisphere (biofilms colonized on plastics) in aquatic ecosystems have drawn increasing attention. Distinct community compositions and structures of biofilms in plastic and natural substrates have been recorded in freshwater environments. However, the microbial metabolic functioning of the plastisphere was underestimated, especially in freshwater environments. In this study, the effects of substrate types on the carbon metabolic functions of biofilms were studied by in situ cultivation of biofilms on plastics (polyvinyl chloride, PVC and polyethylene, PE) and natural substrate (cobblestone) for 44 days in two rivers (the Niushoushan River and the Qinhuai River) and two lakes (Donghu Lake and Xuanwu Lake). Biofilms on plastics showed higher biomasses than those on natural substrates in all ecosystems. Variations in the micro-structure and compactness of biofilms developed under different substrates were observed from scanning electron microscope and confocal laser scanning microscope image analyses. The carbon metabolic activities of the biofilms evaluated by BIOLOG EcoPlate were different between plastics (PVC and PE) and natural substrate (cobblestone) in the four freshwater ecosystems. In the Niushoushan River, PE-associated biofilms had different capacity in using carbon sources from cobblestone-associated biofilms as illustrated by the Shannon-Wiener diversity index and Shannon evenness index. Additionally, the metabolic functional diversity profiles of biofilms on PVC were significantly different from those on cobblestone in the other three aquatic ecosystems. Moreover, results from variation partitioning analysis suggested that the impact of environmental factors (contribution: 21%) on microbial carbon metabolic functions was much greater than that of substrate types (contribution: 6%). These findings illustrated distinct microbial functions of biofilms inhabited on plastics, and environmental factors play a decisive role in the differentiation and specificity of carbon metabolism of the plastisphere. This study offers new insights that plastics serving as artificial microbial niches have the ability to affect the microbial-mediated carbon cycling process in aquatic ecosystems.