Coherent dynamics and association networks among lake bacterioplankton taxa

Interaction and assembly processes of abundant and rare microbial communities during a diatom bloom process

Diatom blooms can significantly influence the dynamics of microbial communities, yet little is known about the interaction and assembly mechanisms of abundant and rare taxa during bloom process. Here, using 16S rRNA gene amplicon sequencing, we investigated the co-occurrence patterns and assembly processes of abundant and rare microbial communities during an early spring diatom bloom in Xiangshan bay. Our results showed that α-diversity indices in the rare subcommunity (RS) were significantly higher than those in the abundant and common subcommunities. β-Diversity of the RS was the highest among three subcommunities, and the variation of β-diversity in the three subcommunities was mainly induced by species turnover, which was also the highest in the RS. The assembly of microbial communities was mainly driven by the neutral processes, but the roles of neutral processes might differ in each subcommunity. Co-occurrence network analysis revealed that abundant and common operational taxonomic units were more often located in central positions within the network. Most of the modules in the network were specific to a particular bloom stage, owing to the succession of Skeletonema costatum. Overall, these findings expand current understanding of the microbial interaction and assembly mechanisms in marine environment suffering harmful algal bloom disturbance.

Habitat Heterogeneity and Connectivity: Effects on the Planktonic Protist Community Structure at Two Adjacent Coastal Sites (the Lagoon and the Gulf of Venice, Northern Adriatic Sea, Italy) Revealed by Metabarcoding

The Lagoon of Venice (LoV) and the Gulf of Venice (GoV), two adjacent coastal Long Term Ecological Research (LTER) sites in the northern Adriatic Sea, represent a transitional/marine coupled ecosystem under the influence of regional and local factors. In this study, these sites were sampled on four dates from April 2016 to February 2017 for environmental DNA and relevant abiotic variables, aiming to assess the relative importance of habitat heterogeneity and connectivity in structuring the protist community. High Throughput Sequencing of V4-18S rRNA gene from 56 samples collected at seven stations produced ca 6 million reads, grouped into 7,336 Operational Taxonomic Units (OTUs) at 97% similarity, which were affiliated to protists belonging to 34 taxonomic groups. The whole community was dominated by Bacillariophyta, especially in spring-summer in the LoV, and by Dinophyta, mainly in the GoV. Ciliophora, Syndiniales, and Cryptophyceae were the next more abundant groups. The community structure varied across the seasons and was different in the two ecosystems, which shared 96% of the reads but showed a high proportion of OTUs distributed preferentially in one of the two sites (specialists) and a different partitioning of trophic categories. GoV specialists were mainly Dinophyceae (>56%), followed by Syndiniales and Bacillariophyta, while the LoV specialists were distributed among several groups, including Bacillariophyta, Syndiniales, Ciliophora, Cryptophyceae, and Trebouxiophyceae. The main abiotic drivers of the differences between protist communities were salinity and temperature, which however explained a minor part of the variance (17%), pointing at a higher relevance of biotic factors and inter-taxa relationships. This was more evident in the LoV, where the network analysis highlighted a higher number of OTUs' connections than in the GoV. Overall, the metabarcoding approach allowed to depict the composition of the whole protist community in the lagoon and adjacent coastal waters with high resolution, revealing many taxa so far not reported in the area. In addition, despite no clear barrier to dispersal processes, differences in the relative abundance and temporal variability of local protist communities indicate that environmental heterogeneity, in these adjacent and connected ecosystems, can be strong enough to allow for ecological segregation.

Co-occurrence patterns of microbial communities affected by inoculants of plant growth-promoting bacteria during phytoremediation of heavy metal-contaminated soils

Phytoremediation assisted by plant growth-promoting bacteria (PGPB) is an alternative method of cleaning up toxic metals from soil. However, the interactions among indigenous soil microorganisms following PGPB inoculation are far from fully understood, although these interactions are conducive to evaluate the effectiveness of PGPB. Here, we used Illumina Miseq sequencing and network analysis to decipher the co-occurrence patterns of bacterial communities following PGPB inoculation during phytoremediation of heavy metal contaminated soil. Miseq sequencing revealed that PGPB inoculation changed the bacterial community composition one day after inoculation, with minor changes continuing to be observed ten days after inoculation. This suggested that PGPB inoculants did not proliferate extensively in a new environment. Network analysis showed that PGPB inoculation altered the co-occurrence patterns, dominant modules and topological roles of individual OTUs. In the presence of PGPB inoculants the bacterial community had more complex and compact associations. Moreover, PGPB inoculation increased the percentage of connectors, indicating that PGPB may contribute to more intensified interactions among OTUs from different modules; consequently, the microbial community would be more ordered and efficient. The enhanced co-occurrence associations in the PGPB-inoculated bacterial network may contribute to the plant growth-promoting effects of PGPB during phytoremediation of heavy metal-contaminated soil.

Niche partitioning of microbial communities in riverine floodplains

Riverine floodplains exhibit high floral and faunal diversity as a consequence of their biophysical complexity. Extension of such niche partitioning processes to microbial communities is far less resolved or supported. Here, we evaluated the responses of aquatic biofilms diversity to environmental gradients across ten riverine floodplains with differing degrees of flow alteration and habitat diversity to assess whether complex floodplains support biofilm communities with greater biodiversity and species interactions. No significant evidence was found to support a central role for habitat diversity in promoting microbial diversity across 116 samples derived from 62 aquatic habitats, as neither α (H': 2.8-4.1) nor β (Sørensen: 0.3-0.39) diversity were positively related to floodplain complexity across the ten floodplains. In contrast, our results documented the sensitivity of biofilm communities to regional templates manifested as gradients of carbon, nitrogen, and phosphorous availability. Large-scale conditions reflecting nitrogen limitation increased the relative abundance of N-fixing cyanobacteria (up to 0.34 as fraction of total reads), constrained the total number of interactions among bacterial taxa, and reinforced negative over positive interactions, generating unique microbial communities and networks that reflect large-scale species sorting in response to regional geochemical gradients.

Dominant role of abundant rather than rare bacterial taxa in maintaining agro-soil microbiomes under environmental disturbances

Elucidating the mechanisms underpinning the responses of abundant and rare microbial taxa to environmental disturbances is essential for understanding the biodiversity-stability relationship and maintaining microbial diversity. Here, we explored the response patterns of abundant and rare bacterial taxa to disturbances by invasive plant growth and oil contamination in agricultural soils across a large spatial scale (latitude gradient = 18.62°-46.51°). Our meta-analysis based on existing Illumina sequencing datasets showed that abundant taxa persisted under the disturbances whereas rare taxa were more easily affected, indicating the higher resilience or resistance of abundant taxa to disturbances. The responses of abundant taxa were associated with mean annual temperature at the sampling sites, while rare taxa instead showed stochastic responses. There were significantly negative linear regressions between bacterial α-diversity and community dissimilarities (disturbed vs. undisturbed soils), suggesting stronger resilience or resistance in those bacterial communities with higher α-diversity. This resilience or resistance was mainly associated with the α-diversity of abundant taxa. Our network analysis showed that the disturbances substantially decreased the strength of the connections, loosened the co-occurrence relationships, and reshaped the complex bacterial interactions. In the undisturbed soils, abundant taxa were located in central positions within the network more often than were rare taxa, while these trends were reversed in the disturbed soils. Our results suggest that abundant taxa play a dominant role in the stability and maintenance of agro-soil bacterial communities, while rare taxa could greatly influence local bacterial interactions under environmental disturbances.

Characterization of Bacterial Communities in Breeding Waters of Anopheles darlingi in Manaus in the Amazon Basin Malaria-Endemic Area

The microbiota in mosquito breeding waters can affect ovipositing mosquitoes, have effects on larval development, and can modify adult mosquito-gut bacterial composition. This, in turn, can affect transmission of human pathogens such as malaria parasites. Here, we explore the microbiota of four breeding sites for Anopheles darlingi, the most important malaria vector in Latin America. The sites are located in Manaus in the Amazon basin in Brazil, an area of active malaria transmission. Using 16S rRNA gene sequencing by MiSeq, we found that all sites were dominated by Proteobacteria and Firmicutes and that 94% of the total number of reads belonged to 36 operational taxonomic units (OTUs) identified in all sites. Of these, the most common OTUs belonged to Escherichia/Shigella, Staphylococcus, and Pseudomonas. Of the remaining 6% of the reads, the OTUs found to differentiate between the four sites belonged to the orders Burkholderiales, Actinomycetales, and Clostridiales. We conclude that An. darlingi can develop in breeding waters with different surface-water bacteria, but that the common microbiota found in all breeding sites might indicate or contribute to a suitable habitat for this important malaria vector.

Coupling of sulfur(thiosulfate)-driven denitratation and anammox process to treat nitrate and ammonium contained wastewater

This study investigated the feasibility of a new biological nitrogen removal process that integrates sulfur-driven autotrophic denitratation (NO₃^-→NO₂^-) and anaerobic ammonium oxidation (Anammox) for simultaneous removal of nitrate and ammonium from industrial wastewater. The proposed sulfur(thiosulfate)-driven denitratation and Anammox process was developed in two phases: First, the thiosulfate-driven denitratation was established in the UASB inoculated with activated sludge and fed with ammonium, nitrate and thiosulfate for 52 days until the nitrite level in the effluent reached 32.1 mg N/L. Second, enriched Anammox biomass was introduced to the UASB to develop the integrated thiosulfate-driven denitratation and Anammox (TDDA) bioprocess (53-212 d). Results showed that nitrate and ammonium could be efficiently removed from synthetic wastewater by the integrated TDDA system at a total nitrogen (TN) removal efficiency of 82.5 ± 1.8% with an influent NH₄⁺-N of 101.2 ± 2.2 mgN/L, NO₃^--N of 101.1 ± 1.5 mgN/L and thiosulfate of 202.5 ± 3.2 mg S/L. It was estimated that Anammox and autotrophic denitritation (NO₂^-→N₂) contributed to about 90% and 10% of the TN removal respectively at stable operation. The established TDDA system was further supported by high-throughput sequencing analysis that sulfur-oxidizing bacteria (e.g., Thiobacillus and Sulfurimonas) coexisted with Anammox bacteria (e.g., Ca. Kuenenia and Ca. Anammoxoglobus) in this syntrophic biocenosis. Additionally, batch experiments were conducted to reveal the kinetic rates and to reconcile the stoichiometry of the electron donor/acceptor couples of the TDDA process. The results unraveled the mechanisms in the new bioprocess: i) sulfite and elemental sulfur (S⁰) were initially generated from branched thiosulfate; ii) oxidation of sulfite and elemental sulfur coupled with fast and slow denitratation; iii) nitrite produced from denitratation together with ammonium were effectively converted to dinitrogen gas via Anammox.

Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China

Revealing the linkages between community assembly and species coexistence, which is crucial for the understanding of ecosystem diversity and functioning, is a fundamental but rarely investigated subject in microbial ecology. Here we examined archaeal, bacterial, and fungal community assembly in adjacent pairs of maize (water-unsaturated) and rice (water-saturated) fields across different habitats and regions throughout Eastern China. The high-throughput sequencing dataset was analyzed by variation partitioning, null model, and neutral community model analyses. We demonstrated that microbial community assembly was governed more by species sorting than by dispersal limitation in maize fields, and to a lesser extent in rice fields. The relative importance of species sorting in maize soils was greater at low latitudes than at high latitudes, while rice soils exhibited an opposite trend. Microbial co-occurrence associations tended to be higher when communities were primarily driven by dispersal limitation relative to species sorting. There were greater community dissimilarities between maize and rice soils in low-latitude regions, which was consistent with the higher proportion of negative edges in the correlation networks. The results indicate that a balance between species sorting and dispersal limitation mediates species coexistence in soil microbiomes. This study enhances our understanding of contemporary coexistence theory in microbial ecosystems.

Obtaining Genome Sequences of Mutualistic Bacteria in Single Microcystis Colonies

Cells of Microcystis are associated with heterotrophic bacteria and organized in colonies in natural environment, which are basic elements in the mass occurrence of cyanobacterial species. Analyzing these colonies by using metagenomics is helpful to understand species composition and relationship. Meanwhile, the difference in population abundance among Microcystis colonies could be used to recover genome bins from metagenome assemblies. Herein, we designed a pipeline to obtain high-quality genomes of mutualistic bacteria from single natural Microcystis colonies. Single colonies were lysed, and then amplified by using multiple displacement amplification to overcome the DNA quantity limit. A two-step assembly was performed after sequencing and scaffolds were grouped into putative bins based on their differential-coverage among species. We analyzed six natural colonies of three prevailing Microcystis species from Lake Taihu. Clustering results proved that colonies of the same species were similar in the microbial community composition. Eight putative population genome bins with wide bacterial diversity and different GC content were identified based on coverage difference among colonies. At the phylum level, proteobacteria was the most abundant besides cyanobacteria. Six of the population bins were further refined into nearly complete genomes (completeness > 90%).

Network Analysis Reveals Seasonal Patterns of Bacterial Community Networks in Lake Taihu under Aquaculture Conditions

Bacterial communities play essential roles in multiple ecological processes, such as primary production and nutrient recycling in aquatic systems. However, although the composition, diversity and function of bacterial communities have been well studied, little is known about the interactions and co-occurrence characteristics of these communities, let alone their seasonal patterns. To investigate the seasonal variations of bacterial community interactions, we collected water samples from four seasons in Lake Taihu and applied network analysis to reveal bacterial community interactions. Bacterial community networks were non-random in structure, and interactions among bacterial taxa in the networks varied markedly in different seasons. The autumnal bacterial network was the largest and most complex among obtained networks, whereas the spring correlation network was the simplest, having no module hubs or connectors. The important species of the networks were the dominant bacterial phyla/classes (e.g., Alphaproteobacteria and Bacteroidetes), although their relative abundance varied among seasons. The relationships between species and measured environmental variables changed over seasons; fewer environmental factors were correlated with bacterial species in the spring bacterial network, while we observed a greater number of species-environment correlations in the winter network. Our study highlights the seasonal differences in bacterial community interactions and expands our understanding of freshwater microbial ecology in systems affected by aquaculture.

Performance and bacterial community of moving bed biofilm reactors with various biocarriers treating primary wastewater effluent with a low organic strength and low C/N ratio

A laboratory-scale sequencing batch reactor (SBR) and two moving bed biofilm reactors (MBBRs) with different types of biocarriers were operated to treat the effluent of chemically enhanced primary sedimentation (CEPS). Due to the low organic strength and low carbon/nitrogen ratio of the CEPS effluent, COD and NH₄⁺-N were effectively removed by the MBBRs but not by the SBR. Of the two MBBRs, MBBR2 filled with LEVAPOR biocarrier cubes performed even better than MBBR1 filled with K3 polystyrene biocarriers. The continuous decline of the sludge concentration in the SBR and the high and stable biomass content in MBBR2 contributed to their performances. High-throughput sequencing analysis showed that the reactors had selective effects on the bacterial community structure. Principal coordinate analysis indicated the different dynamic successions in the three reactors. Network analysis showed different community composition and diversity that were highly suggestive of different bacterial interactions among the three bioreactors.

Microdiversity ensures the maintenance of functional microbial communities under changing environmental conditions

Microdiversity can lead to different ecotypes within the same species. These are assumed to provide stability in time and space to those species. However, the role of microdiversity in the stability of whole microbial communities remains underexplored. Understanding the drivers of microbial community stability is necessary to predict community response to future disturbances. Here, we analyzed 16S rRNA gene amplicons from eight different temperate bog lakes at the 97% OTU and amplicon sequence variant (ASV) levels and found ecotypes within the same OTU with different distribution patterns in space and time. We observed that these ecotypes are adapted to different values of environmental factors such as water temperature and oxygen concentration. Our results showed that the existence of several ASVs within a OTU favored its persistence across changing environmental conditions. We propose that microdiversity aids the stability of microbial communities in the face of fluctuations in environmental factors.

Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System

Caves are typified by their permanent darkness and a shortage of nutrients. Consequently, bacteria play an important role in sustaining such subsurface ecosystems by dominating primary production and fueling biogeochemical cycles. China has one of the world’s largest areas of karst topography in the Yunnan-Guizhou Plateau, yet the bacteriomes in these karst caves remain unexplored. In this study, bacteriomes of eight karst caves in southwest China were examined, and co-occurrence networks of cave bacterial communities were constructed. Results revealed abundant and diversified bacterial communities in karst caves, with Proteobacteria, Actinobacteria, and Firmicutes being the most abundant phyla. Statistical analysis revealed no significant difference in bacteriomes among the eight caves. However, a PCoA plot did show that the bacterial communities of 128 cave samples clustered into groups corresponding to sampling types (air, water, rock, and sediment). These results suggest that the distribution of bacterial communities is driven more by sample types than the separate caves from which samples were collected. Further community-level composition analysis indicated that Proteobacteria were most dominant in water and air samples, while Actinobacteria dominated the sediment and rock samples. Co-occurrence analysis revealed highly modularized assembly patterns of the cave bacterial community, with Nitrosococcaceae wb1-P19, an uncultured group in Rokubacteriales, and an uncultured group in Gaiellales, being the top-three keystone members. These results not only expand our understanding of cave bacteriomes but also inspires functional exploration of bacterial strains in karst caves.

Characterization of Distinct CyanoHABs-Related Modules in Microbial Recurrent Association Network

To elucidate the interspecies connectivity between cyanobacteria and other bacteria (non-cyanobacteria) during cyanobacterial harmful algal blooms (cyanoHABs), samples were collected from the Nakdong River, Korea, from June 2016 to August 2017, and microbial recurrent association network (MRAN) analysis was performed to overcome the limitations of conventional network analysis. Microcystis blooms were tightly linked with Pseudanabaena in summer and were accompanied by significant changes in the non-cyanobacterial community composition (nCCC) compared to non-bloom period. Riverine bacterial communities could be clearly separated into modules that were involved in the formation, maintenance, and decomposition of cyanoHABs. Roseomonas and Herbaspirillum were directly linked with major cyanobacteria and assigned to connector and module hub in cyanoHABs-related modules, respectively. The functional profiles of the cyanoHABs-related modules suggested that nitrate reduction, aerobic ammonia oxidation, fermentation, and hydrocarbon degradation could be increased during the Microcystis bloom periods. In conclusion, MRAN analysis revealed that specific bacteria belonging to cyanoHABs-related module, including connectors and module hubs, appeared to contribute to the development and collapse of cyanoHABs. Therefore, to understand cyanoHABs, a modular microbial perspective may be more helpful than a single bacterial species perspective.

Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems

Microbial community assembly in engineered biological systems is often simultaneously influenced by stochastic and deterministic processes, and the nexus of these two mechanisms remains to be further investigated. Here, three lab-scale activated sludge reactors were seeded with identical inoculum and operated in parallel under eight different sludge retention time (SRT) by sequentially reducing the SRT from 15 days to 1 day. Using 16S rRNA gene amplicon sequencing data, the microbial populations at the start-up (15-day SRT) and SRT-driven (≤10-day SRT) phases were observed to be noticeably different. Clustering results demonstrated ecological succession at the start-up phase with no consistent successional steps among the three reactors, suggesting that stochastic processes played an important role in the community assembly during primary succession. At the SRT-driven phase, the three reactors shared 31 core operational taxonomic units (OTUs). Putative primary acetate utilizers and secondary metabolizers were proposed based on K-means clustering, network and synchrony analysis. The shared core populations accounted for 65% of the total abundance, indicating that the microbial communities at the SRT-driven phase were shaped predominantly by deterministic processes. Sloan’s Neutral model and a null model analysis were performed to disentangle and quantify the relative influence of stochastic and deterministic processes on community assembly. The increased estimated migration rate in the neutral community model and the higher percentage of stochasticity in the null model implied that stochastic community assembly was intensified by strong deterministic factors. This was confirmed by the significantly different α- and β-diversity indices at SRTs shorter than 2 days and the observation that over half of the core OTUs were unshared or unsynchronized. Overall, this study provided quantitative insights into the nexus of stochastic and deterministic processes on microbial community assembly in a biological process.

Inference of Environmental Factor-Microbe and Microbe-Microbe Associations from Metagenomic Data Using a Hierarchical Bayesian Statistical Model

The inference of associations between environmental factors and microbes and among microbes is critical to interpreting metagenomic data, but compositional bias, indirect associations resulting from common factors, and variance within metagenomic sequencing data limit the discovery of associations. To account for these problems, we propose metagenomic Lognormal-Dirichlet-Multinomial (mLDM), a hierarchical Bayesian model with sparsity constraints, to estimate absolute microbial abundance and simultaneously infer both conditionally dependent associations among microbes and direct associations between microbes and environmental factors. We empirically show the effectiveness of the mLDM model using synthetic data, data from the TARA Oceans project, and a colorectal cancer dataset. Finally, we apply mLDM to 16S sequencing data from the western English Channel and report several associations. Our model can be used on both natural environmental and human metagenomic datasets, promoting the understanding of associations in the microbial community.

Biostimulation of in situ microbial degradation processes in organically-enriched sediments mitigates the impact of aquaculture

Fish farm deposition, resulting in organic matter accumulation on bottom sediments, has been identified as among the main phenomena causing negative environmental impacts in aquaculture. An in situ bioremediation treatment was carried out in order to reduce the organic matter accumulation in the fish farm sediments by promoting the natural microbial biodegradation processes. To assess the effect of the treatment, the concentration of organic matter in the sediment and its microbial degradation, as well as the response of the benthic prokaryotic community, were investigated. The results showed a significant effect of the treatment in stimulating microbial degradation rates, and the consequent decrease in the concentration of biochemical components beneath the cages during the treatment. During the bioremediation process, the prokaryotic community in the fish farm sediment responded to the overall improvement of the sediment conditions by showing the decrease of certain anaerobic taxa (e.g. Clostridiales, Acidaminobacteraceae and Caldilinaceae). This suggested that the bioactivator was effective in promoting a shift from an anaerobic to an aerobic metabolism in the prokaryotic community. However, the larger importance of Lachnospiraceae (members of the gut and faecal microbiota of the farmed fishes) in treated compared to non-treated sediments suggested that the bioactivator was not efficient in reducing the accumulation of faecal bacteria from the farmed fishes. Our results indicate that bioremediation is a promising tool to mitigate the aquaculture impact in fish farm sediments, and that further research needs to be oriented to identifying more successful interventions able to specifically target also fish-faeces related microbes.

An integrated insight into the response of bacterial communities to anthropogenic contaminants in a river: A case study of the Wonderfonteinspruit catchment area, South Africa

Bacterial communities in human-impacted rivers and streams are exposed to multiple anthropogenic contaminants, which can eventually lead to biodiversity loss and function. The Wonderfonteinspruit catchment area is impacted by operational and abandoned gold mines, farms, and formal and informal settlements. In this study, we used 16S rRNA gene high-throughput sequencing to characterize bacterial communities in the lower Wonderfonteinspruit and their response to various contaminant sources. The results showed that composition and structure of bacterial communities differed significantly (P<0.05) between less (downstream) and more (upstream) polluted sites. The taxonomic and functional gene dissimilarities significantly correlated with each other, while downstream sites had more distinct functional genes. The relative abundance of Proteobacteria, Bacteroidetes and Actinobacteria was higher at upstream sites, while Acidobacteria, Cyanobacteria, Firmicutes and Verrucomicrobia were prominent at downstream sites. In addition, upstream sites were rich in genera pathogenic and/or potentially pathogenic to humans. Multivariate and correlation analyses suggest that bacterial diversity was significantly (P<0.05) impacted by pH and heavy metals (cobalt, arsenic, chromium, nickel and uranium). A significant fraction (~14%) of the compositional variation was explained by a combination of anthropogenic inputs, of which mining (~6%) was the main contributor to bacterial community variation. Network analysis indicated that bacterial communities had non-random inter- and intra-phyla associations and that the main taxa showed both positive and negative linkages to environmental parameters. Our results suggest that species sorting, due to environmental parameters, was the main process that structured bacterial communities. Furthermore, upstream sites had higher relative abundances of genes involved in xenobiotic degradation, suggesting stronger removal of polycyclic aromatic hydrocarbons and other organic compounds. This study provides insights into the influences of anthropogenic land use on bacterial community structure and functions in the lower Wonderfonteinspruit.

Stepwise pH control to promote synergy of chemical and biological processes for augmenting short-chain fatty acid production from anaerobic sludge fermentation

Although sludge-converted short-chain fatty acids (SCFAs) are promising feedstocks for biorefineries, it remains challenging to maximise SCFA production by enhancing synergies between chemical/biological hydrolysis and acidogenesis processes while employing a balanced composition of microbial communities to counteract methanogenesis. Herein, stepwise control of fermentation pH and chemical/microbiological composition analysis of fermented sludge were used to probe the underlying mechanisms of SCFA production. Fermentation at pH 11 during the first three days promoted both chemical and microbial hydrolysis of sludge proteins and provided a niche for Anaerobrancaceae sp. to transform soluble protein into SCFAs. When pH was decreased from 11 to 9, Acinetobacter, Proteiniborus, Proteiniclasticum, and other acetogens became predominant and stayed significantly more active than during first-stage fermentation at pH 11, which benefited the acidification of hydrolysed substrates. Further assays indicated that early-stage sludge fermentation at pH 11 decreased the total amount of methanogenic archaea and hence reduced the amount of SCFAs consumed for methane production. Thus, the use of stepwise pH control for sludge fermentation allowed one to establish process synergies, facilitate chemical and biological hydrolysis, inhibit methanogens, and promote the growth of acidifying bacterial communities, which resulted in efficient SCFA production from sludge.

Influence of Environmental Drivers and Potential Interactions on the Distribution of Microbial Communities From Three Permanently Stratified Antarctic Lakes

The McMurdo Dry Valley (MDV) lakes represent unique habitats in the microbial world. Perennial ice covers protect liquid water columns from either significant allochthonous inputs or seasonal mixing, resulting in centuries of stable biogeochemistry. Extreme environmental conditions including low seasonal photosynthetically active radiation (PAR), near freezing temperatures, and oligotrophy have precluded higher trophic levels from the food webs. Despite these limitations, diverse microbial life flourishes in the stratified water columns, including Archaea, bacteria, fungi, protists, and viruses. While a few recent studies have applied next generation sequencing, a thorough understanding of the MDV lake microbial diversity and community structure is currently lacking. Here we used Illumina MiSeq sequencing of the 16S and 18S rRNA genes combined with a microscopic survey of key eukaryotes to compare the community structure and potential interactions among the bacterial and eukaryal communities within the water columns of Lakes Bonney (east and west lobes, ELB, and WLB, respectively) and Fryxell (FRX). Communities were distinct between the upper, oxic layers and the dark, anoxic waters, particularly among the bacterial communities residing in WLB and FRX. Both eukaryal and bacterial community structure was influenced by different biogeochemical parameters in the oxic and anoxic zones. Bacteria formed complex interaction networks which were lake-specific. Several eukaryotes exhibit potential interactions with bacteria in ELB and WLB, while interactions between these groups in the more productive FRX were relatively rare.

Leaf and Root Endospheres Harbor Lower Fungal Diversity and Less Complex Fungal Co-occurrence Patterns Than Rhizosphere

Plant-associated microbiomes are key determinants of host-plant fitness, productivity, and function. However, compared to bacterial community, we still lack fundamental knowledge concerning the variation in the fungal microbiome at the plant niche level. In this study, we quantified the fungal communities in the rhizosphere soil, as well as leaf and root endosphere compartments of a subtropical island shrub, Mussaenda kwangtungensis, using high-throughput DNA sequencing. We found that fungal microbiomes varied significantly across different plant compartments. Rhizosphere soil exhibited the highest level of fungal diversity, whereas the lowest level was found in the leaf endosphere. Further, the fungal communities inhabiting the root endosphere shared a greater proportion of fungal operational taxonomic units (OTUs) with rhizosphere communities than with leaf fungal endophyte communities, despite significant separation in community structure between the two belowground compartments. The fungal co-occurrence networks in the three compartments of M. kwangtungensis showed scale-free features and non-random co-occurrence patterns and matched the topological properties of small-world and evidently modular structure. Additionally, the rhizosphere network was more complex and showed higher centrality and connectedness than the leaf and root endosphere networks. Overall, our findings provide comprehensive insights into the structural variability, niche differentiation, and co-occurrence patterns in the plant associated fungal microbiome.

Black soldier fly larvae (Hermetia illucens) strengthen the metabolic function of food waste biodegradation by gut microbiome

Vermicomposting using black soldier fly (BSF) larvae (Hermetia illucens) has gradually become a promising biotechnology for waste management, but knowledge about the larvae gut microbiome is sparse. In this study, 16S rRNA sequencing, SourceTracker, and network analysis were leveraged to decipher the influence of larvae gut microbiome on food waste (FW) biodegradation. The microbial community structure of BSF vermicompost (BC) changed greatly after larvae inoculation, with a peak colonization traceable to gut bacteria of 66.0%. The relative abundance of 11 out of 21 metabolic function groups in BC were significantly higher than that in natural composting (NC), such as carbohydrate-active enzymes. In addition, 36.5% of the functional genes in BC were significantly higher than those in NC. The changes of metabolic functions and functional genes were significantly correlated with the microbial succession. Moreover, the bacteria that proliferated in vermicompost, including Corynebacterium, Vagococcus, and Providencia, had strong metabolic abilities. Systematic and complex interactions between the BSF gut and BC bacteria occurred over time through invasion, altered the microbial community structure, and thus evolved into a new intermediate niche favourable for FW biodegradation. The study highlights BSF gut microbiome as an engine for FW bioconversion, which is conducive to bioproducts regeneration from wastes.

Influence of Environmental and Anthropogenic Factors on Microbial Ecology and Sanitary Threat in the Final Stretch of the Brda River

Ecology of aquatic microorganisms depends on a number of environmental parameters. The additional influence of anthropogenic factors is connected with sanitary risk, particularly in urban areas. The study was aimed at assessing the impact of physicochemical and biological parameters on the abundance and activity of bacterioplankton under different spatio-temporal conditions in the urbanized section of the Brda River. The evaluation of sanitary pollution of water was accompanied by the assessment of antibiotic resistance of isolated faecal strains determined using the disk diffusion method. The results indicate that the location of sampling sites significantly affected by the distribution of faecal Escherichia coli and enterococci in the studied part of the river. On the other hand, there were no significant seasonal changes in respiratory activity or abundance of planktonic bacteria. In addition, the abundance of bacterioplankton was not correlated with all measured physico-chemical parameters, though it was correlated with the organic carbon oxidation rate. Depending on the sampling site, bacterial cells with damaged membranes constituted between 8% and 20% of the population. Antibiograms showed the absence of multi-drug resistant strains. Enterococci exhibited the highest resistance to imipenem (45%), while Escherichia coli, to cefoxitin (31%).

Presence of Aedes and Anopheles mosquito larvae is correlated to bacteria found in domestic water-storage containers

Water-storage containers are common in households where access to water is scarce and often act as breeding sites for vector mosquitoes. Bacteria in these containers may be important for attracting or repelling ovipositing mosquitoes. We hypothesized that bacterial community composition in water-storage containers would represent either inhibitory or suitable environmental conditions for mosquito larvae. To investigate this, we characterized the bacterial community composition in water-storage containers and correlated these communities to Aedes and Anopheles larval densities. Water samples were collected over two years from 13 containers in an Indian village and analyzed by high throughput 16S rRNA gene amplicon sequencing. Comparisons of bacterial community composition between water with and without mosquito larvae showed that Xanthomonadaceae, Comamonadaceae and Burkholderiaceae were more common (P < 0.05) in absence of larvae, while Lachnospiraceae, Synechococcaceae, Alcaligenaceae and Cryomorphaceae were more common (P < 0.05) in presence of larvae. Indicator analysis identified operational taxonomic units designated as CL500-29 marine group (Acidimicrobiaceae) and FukuN101 (Microbacteriaceae) for absence and presence of larvae, respectively. These results contribute to the understanding of which bacteria, directly or indirectly, can be linked to absence or presence of mosquitoes around households and set the basis for potential measures to be taken against these vector mosquitoes.

Co-occurrence patterns of the microbial community in polycyclic aromatic hydrocarbon-contaminated riverine sediments

Understanding environmental and spatial gradient influences on sediment microbial communities, especially the communities of highly contaminated subsurface sediments, has received great attention with respect to natural attenuation and bioremediation. Here, we investigated the spatial variation and the co-occurrence patterns of microbial communities in polycyclic aromatic hydrocarbon (PAH)-contaminated riverine sediments by using spatial-series 16S rRNA gene data. The results showed that species from the surface and subsurface sediment samples tended to show greater co-occurrence patterns and facilitative interactions in the sediment microbial community as environmental severity increased. Microorganisms in the heavier PAH-contaminated sediment have stronger relationships and are more centrally clustered within the network compared to microorganisms in the lower PAH-contaminated sediment. The core communities harbored the keystone species (Dechloromonas, Crenothrix, Desulfuromonadales, Xanthomonadales, Anaerolineaceae and Dehalococcoidales), which responded to changes in the environmental and spatial gradients. The sediment PAH concentrations, ferrous iron and vertical distance were identified as the main drivers in determining the bacterial community assembly. The keystone species were linked to PAHs biodegradation coupled with iron cycling in sediments and could orchestrate core communities to perform ecosystem processes. Overall, these findings provide new insight into microbial community assembly and contribute to harnessing their functions in ecosystems for bioremediation.

Co-occurrence patterns between phytoplankton and bacterioplankton across the pelagic zone of Lake Baikal during spring

Phytoplankton and bacterioplankton play a key role in carbon cycling of aquatic ecosystems. In this study, we found that co-occurrence patterns between different types of phytoplankton, bacterioplankton, and environmental parameters in Lake Baikal during spring were different over the course of three consecutive years. The composition of phytoplankton and bacterial communities was investigated using microscopy and 16S rRNA gene pyrosequencing, respectively. Non-metric multidimensional scaling (NMDS) revealed a relationship between the structure of phytoplankton and bacterial communities and temperature, location, and sampling year. Associations of bacteria with diatoms, green microalgae, chrysophyte, and cryptophyte were identified using microscopy. Cluster analysis revealed similar correlation patterns between phytoplankton abundance, number of attached bacteria, ratio of bacteria per phytoplankton cell and environmental parameters. Positive and negative correlations between different species of phytoplankton, heterotrophic bacteria and environmental parameters may indicate mutualistic or competitive relationships between microorganisms and their preferences to the environment.

Core Microbiota in Agricultural Soils and Their Potential Associations with Nutrient Cycling

Disentangling the roles of the core microbiota in community maintaining and soil nutrient cycling is an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the spatial atlas and ecological roles of the core microbiota. A systematic, continental-scale survey was conducted using agro-soils in adjacent pairs of maize (dryland) and rice (wetland) fields across eastern China. The results indicate that the core microbiota play major ecological roles in maintaining complex connections between bacterial taxa and are associated with belowground multinutrient cycling. A continental atlas was built for mapping the bacterial spatial distributions in agro-soils through identifying their habitat preferences. This study represents a significant advance in forecasting the responses of agricultural ecosystems to anthropogenic disturbance and thus helps manage soil bacterial communities for better provisioning of key ecosystem services—the ultimate goal of microbial ecology.

Revealing the ecological roles of the core microbiota in community maintaining and soil nutrient cycling is crucial for understanding ecosystem function, yet there is a dearth of continental-scale studies on this fundamental topic in microbial ecology. Here, we collected 251 soil samples from adjacent pairs of maize and rice fields at a continental scale in eastern China. We revealed the major ecological roles of the core microbiota in maintaining complex connections between bacterial taxa and their associations with belowground multinutrient cycling. By identifying the habitat preferences of the core microbiota, we built a continental atlas for mapping the spatial distributions of bacteria in agro-soils, which helps forecast the responses of agricultural ecosystems to anthropogenic disturbance. The multinutrient cycling index for maize and rice soils was related to bacterial α-diversity and β-diversity, respectively. Rice soils exhibited higher bacterial diversity and closer bacterial cooccurrence relationships than maize soils. In contrast to the macro- or microecological latitudinal richness patterns in natural terrestrial ecosystems, the bacteria in maize soils showed higher richness at high latitudes; however, this trend was not observed in rice soils. This study provides a new perspective on the distinct bacterial biogeographic patterns to predict the ecological roles of the core microbiota in agro-soils and thus helps manage soil bacterial communities for better provisioning of key ecosystem services.

IMPORTANCE Disentangling the roles of the core microbiota in community maintaining and soil nutrient cycling is an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the spatial atlas and ecological roles of the core microbiota. A systematic, continental-scale survey was conducted using agro-soils in adjacent pairs of maize (dryland) and rice (wetland) fields across eastern China. The results indicate that the core microbiota play major ecological roles in maintaining complex connections between bacterial taxa and are associated with belowground multinutrient cycling. A continental atlas was built for mapping the bacterial spatial distributions in agro-soils through identifying their habitat preferences. This study represents a significant advance in forecasting the responses of agricultural ecosystems to anthropogenic disturbance and thus helps manage soil bacterial communities for better provisioning of key ecosystem services—the ultimate goal of microbial ecology.

Spatio-temporal dynamics of sulfur bacteria during oxic--anoxic regime shifts in a seasonally stratified lake

Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria drive major transformations in the sulfur cycle, and play vital roles in oxic--anoxic transitions in lakes and coastal waters. However, information on the succession of these sulfur bacteria in seasonally stratified lakes using molecular biological techniques is scarce. Here, we used 16S rRNA gene amplicon sequencing to study the spatio-temporal dynamics of sulfur bacteria during oxic--anoxic regime shifts in Lake Vechten. Oxygen and sulfate were mixed throughout the water column in winter and early spring. Meanwhile, SRB, green sulfur bacteria (GSB), purple sulfur bacteria (PSB), and colorless sulfur bacteria (CSB) exclusively inhabited the sediment. After the water column stratified, oxygen and nitrate concentrations decreased in the hypolimnion and various SRB species expanded into the anoxic hypolimnion. Consequently, sulfate was reduced to sulfide, stimulating the growth of PSB and GSB in the metalimnion and hypolimnion during summer stratification. When hypoxia spread throughout the water column during fall turnover, SRB and GSB vanished from the water column, whereas CSB (mainly Arcobacter) and PSB (Lamprocystis) became dominant and oxidized the accumulated sulfide under micro-aerobic conditions. Our results support the view that, once ecosystems have become anoxic and sulfidic, a large oxygen influx is needed to overcome the anaerobic sulfur cycle and bring the ecosystems back into their oxic state.

Changes in Bacterioplankton Communities Resulting From Direct and Indirect Interactions With Trace Metal Gradients in an Urbanized Marine Coastal Area

Unraveling the relative importance of both environmental conditions and ecological processes regulating bacterioplankton communities is a central goal in microbial ecology. Marine coastal environments are among the most urbanized areas and as a consequence experience environmental pressures. The highly anthropized Toulon Bay (France) was considered as a model system to investigate shifts in bacterioplankton communities along natural and anthropogenic physicochemical gradients during a 1-month survey. In depth geochemical characterization mainly revealed strong and progressive Cd, Zn, Cu, and Pb contamination gradients between the entrance of the Bay and the north-western anthropized area. On the other hand, low-amplitude natural gradients were observed for other environmental variables. Using 16S rRNA gene sequencing, we observed strong spatial patterns in bacterioplankton taxonomic and predicted function structure along the chemical contamination gradient. Variation partitioning analysis demonstrated that multiple metallic contamination explained the largest part of the spatial biological variations observed, but DOC and salinity were also significant contributors. Network analysis revealed that biotic interactions were far more numerous than direct interactions between microbial groups and environmental variables. This suggests indirect effects of the environment, and especially trace metals, on the community through a few taxonomic groups. These spatial patterns were also partially found for predicted bacterioplankton functions, thus indicating a limited functional redundancy. All these results highlight both potential direct influences of trace metals contamination on coastal bacterioplankton and indirect forcing through biotic interactions and cascading.

Seasonal, sub-seasonal and diurnal variation of soil bacterial community composition in a temperate deciduous forest

The temporal dynamics of soil bacterial communities are understudied, but such understanding is critical to elucidating the drivers of community variation. The goal of this study was to characterize how soil bacterial communities vary across diurnal, sub-seasonal and seasonal time-scales in a 5.8 m2 plot and test the hypothesis that bacterial diversity varies on each of these scales. We used 16S rDNA gene amplicon sequencing to quantify the alpha and beta diversity of soil bacteria as well as the Net Relatedness Index and Nearest Taxon Indices to assess the degree of phylogenetic clustering, and the extent to which community shifts were driven by stochastic vs. deterministic limitation. We found that species richness was highest in winter, lowest in fall and that communities were compositionally distinct across seasons. There was no evidence of diurnal-scale shifts; the finest temporal scale over which community shifts were detected using our DNA-based analysis was between sampling dates separated by 6 weeks. Phylogenetic analyses suggested that seasonal-scale differences in community composition were the result of environmental filtering and homogeneous selection. Our findings provide insight into temporal variation of soil bacterial communities across the hourly to seasonal scales while minimizing the potential confounding effect of spatial variation.

Differential co-occurrence relationships shaping ecotype diversification within Thaumarchaeota populations in the coastal ocean water column

Ecological factors contributing to depth-related diversification of marine Thaumarchaeota populations remain largely unresolved. To investigate the role of potential microbial associations in shaping thaumarchaeal ecotype diversification, we examined co-occurrence relationships in a community composition dataset (16S rRNA V4-V5 region) collected as part of a 2-year time series in coastal Monterey Bay. Ecotype groups previously defined based on functional gene diversity-water column A (WCA), water column B (WCB) and Nitrosopumilus-like clusters-were recovered in the thaumarchaeal 16S rRNA gene phylogeny. Networks systematically reflected depth-related patterns in the abundances of ecotype populations, suggesting thaumarchaeal ecotypes as keystone members of the microbial community below the euphotic zone. Differential environmental controls on the ecotype populations were further evident in subnetwork modules showing preferential co-occurrence of OTUs belonging to the same ecotype cluster. Correlated abundances of Thaumarchaeota and heterotrophic bacteria (e.g., Bacteroidetes, Marinimicrobia and Gammaproteobacteria) indicated potential reciprocal interactions via dissolved organic matter transformations. Notably, the networks recovered ecotype-specific associations between thaumarchaeal and Nitrospina OTUs. Even at depths where WCB-like Thaumarchaeota dominated, Nitrospina OTUs were found to preferentially co-occur with WCA-like and Nitrosopumilus-like thaumarchaeal OTUs, highlighting the need to investigate the ecological implications of the composition of nitrifier assemblages in marine waters.

Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom

The pelagic zone of Lake Baikal is an ecological niche where phytoplankton bloom causes increasing microbial abundance in spring which plays a key role in carbon turnover in the freshwater lake. Co-occurrence patterns revealed among different microbes can be applied to predict interactions between the microbes and environmental conditions in the ecosystem. We used 454 pyrosequencing of 16S rRNA and 18S rRNA genes to study bacterial and microbial eukaryotic communities and their co-occurrence patterns at the pelagic zone of Lake Baikal during a spring phytoplankton bloom. We found that microbes within one domain mostly correlated positively with each other and are highly interconnected. The highly connected taxa in co-occurrence networks were operational taxonomic units (OTUs) of Actinobacteria, Bacteroidetes, Alphaproteobacteria, and autotrophic and unclassified Eukaryota which might be analogous to microbial keystone taxa. Constrained correspondence analysis revealed the relationships of bacterial and microbial eukaryotic communities with geographical location.

Characterization of airborne antibiotic resistance genes from typical bioaerosol emission sources in the urban environment using metagenomic approach

The wide spread of antibiotic resistance genes (ARGs) has attracted increasing concern. However, the occurrence and diversity of ARGs in airborne particles remains to be understood. In this study, total suspended particles (TSP) in the atmosphere were collected from typical sources of ARG pollution, including animal farms and wastewater treatment plant (WWTP), as well as the downtown area in Zhuhai, China. Metagenomic profiling demonstrated that ARGs were abundant and diverse in the TSP from animal farms and WWTP, but significant differences in ARG composition pattern between these samples were observed. ARGs associated with the resistance to aminoglycoside, macrolide-lincosamide-streptogramin (MLS) and tetracycline were dominant over other ARGs in the TSP of the animal farms, whereas multidrug and bacitracin resistance genes were more abundant than other ARGs in the TSP of the WWTP. In the animal farms, ARG profiles of the TSP were consistent with those of animal feces, indicating that animal feces could be one of the most contributing sources of airborne ARGs in animal farms. In contrast to representative sources of ARG pollution, ARG abundance and diversity in the TSP collected from the downtown area was relatively low, with multidrug resistance genes being predominant. This study suggests that metagenomic profiling of the ARGs in airborne TSP could enhance our comprehensive understanding of ARGs dissemination in the environment and their potential health threats.

Dynamics of Sediment Microbial Functional Capacity and Community Interaction Networks in an Urbanized Coastal Estuary

Coastal estuaries and bays are exposed to both natural and anthropogenic environmental changes, inflicting intensive stress on the microbial communities inhabiting these areas. However, it remains unclear how microbial community diversity and their eco-functions are affected by anthropogenic disturbances rather than natural environmental changes. Here, we explored sediment microbial functional genes dynamics and community interaction networks in Hangzhou Bay (HZB), one of the most severely polluted bays on China’s eastern coast. The results indicated key microbial functional gene categories, including N, P, S, and aromatic compound metabolism, and stress response, displayed significant spatial dynamics along environmental gradients. Sensitive feedbacks of key functional gene categories to N and P pollutants demonstrated potential impacts of human-induced seawater pollutants to microbial functional capacity. Seawater ammonia and dissolved inorganic nitrogen (DIN) was identified as primary drivers in selecting adaptive populations and varying community composition. Network analysis revealed distinct modules that were stimulated in inner or outer bay. Importantly, the network keystone species, which played a fundamental role in community interactions, were strongly affected by N-pollutants. Our results provide a systematic understanding of the microbial compositional and functional dynamics in an urbanized coastal estuary, and highlighted the impact of human activities on these communities.

Competitive lottery-based assembly of selected clades in the human gut microbiome

BACKGROUND

While the composition of the gut microbiome has now been well described by several large-scale studies, models that can account for the range of microbiome compositions that have been observed are still lacking. One model that has been well studied in macro communities and that could be useful for understanding microbiome assembly is the competitive lottery model. This model posits that groups of organisms from a regional pool of species are able to colonize the same niche and that the first species to arrive will take over the entire niche, excluding other group members.

RESULTS

Here, we examined whether this model also plays a role in the assembly of the human gut microbiome, defining measures to identify groups of organisms whose distribution across samples conforms to the competitive lottery schema. Applying this model to multiple datasets with thousands of human gut microbiome samples, we identified several taxonomic groups that exhibit a lottery-like distribution, including the Akkermansia, Dialister, and Phascolarctobacterium genera. We validated that these groups exhibit lottery-like assembly in multiple independent microbiome datasets confirming that this assembly schema is universal and not cohort specific. Examining the distribution of species from these groups in the gut microbiome of developing infants, we found that the initial lottery winner can be replaced by a different member of the group. We further found that species from lottery-like groups tend to have fewer genes in their genomes, suggesting more specialized species that are less able to engage in niche differentiation.

CONCLUSIONS

Combined, our findings highlight the complex and dynamic process through which microbial communities assemble and suggest that different phylogenetic groups may follow different models during this process.

How bacterioplankton community can go with cascade damming in the highly regulated Lancang-Mekong River Basin

Rivers make vital contributions to the transport of water, sediment and nutrients from terrestrial to marine ecosystems. However, many large rivers worldwide are suffering from dam regulation. Increasing attention has been paid to bacterioplankton communities since they are highly responsive to river alterations and may influence biogeochemical processes. Here, a comprehensive study was conducted in the highly regulated Lancang-Mekong River Basin to address the question of how bacterioplankton communities respond to cascade damming. The results showed that dam constructions increased nutrient concentrations and threatened water quality in cascade reservoirs. Bacterioplankton cell abundance was reduced by damming, and α-diversity was inhibited in cascade reservoirs. Fortunately, however, river ecosystems were resilient after the remarkable disturbance caused by damming. Moreover, bacterioplankton community composition was significantly altered by cascade dams, including a shift in the dominant phylum from r-strategists to k-strategists. Meanwhile, according to GeoChip analysis, the functional composition of bacterioplankton was less affected than taxonomic composition. In addition, geographic and environmental features both followed a distance-decay relationship with community and functional composition, but the local environment condition was the dominant driver in the Lancang River. Therefore, the impoundments of cascade dams had significant impacts on bacterioplankton communities and more attention should be paid to the potential ecological consequences of river regulation.

Shifts in community composition and co-occurrence patterns of phyllosphere fungi inhabiting Mussaenda shikokiana along an elevation gradient

The altitudinal effects on the distributions of phyllosphere fungal assemblages in conspecific plants remain poorly elucidated. To address this, phyllosphere fungal communities associated with Mussaenda shikokiana were investigated at four sites across a 350 m elevation gradient in a subtropical forest by employing Illumina metabarcoding of the fungal internal transcribed spacer 2 (ITS2) region. Our results demonstrated that phyllosphere fungal assemblages with a single host possessed high taxonomic diversity and multiple trophic guilds. OTU richness was significantly influenced by elevation. The elevation gradient also entailed distinct shifts in the community composition of phyllosphere fungi, which was significantly related to geographical distance and mean annual temperature (MAT). Additionally, comparison of phyllosphere fungal networks showed reduced connectivity with increasing elevation. Our data provide insights on the distribution and interactions of the phyllosphere fungal community associated with a single host along a short elevation gradient.

Exploring the microbiome of the "star" freshwater diatom Asterionella formosa in a laboratory context

Most of our knowledge on the mechanisms underlying diatom-bacterial interactions has been acquired through studies involving isolation of culturable partners. Here, we established a laboratory model of intermediate complexity between complex natural communities and laboratory pure culture models. We investigated the whole community formed by the freshwater diatom Asterionella formosa and its associated bacteria in a laboratory context, including both culturable and unculturable bacteria. Combining cellular and molecular approaches, we showed that in laboratory cultures, A. formosa microbiome was dynamic and comprised of numerous bacterial species (mainly Proteobacteria and Bacteroidetes). Using metagenomics, we explored several metabolic potentials present within the bacterial community. Our analyses suggested that bacteria were heterotrophic although a third of them (Alpha- and Beta-proteobacteria) could also be phototrophic. About 60% of the bacteria, phylogenetically diverse, could metabolize glycolate. The capacity to synthesize molecules such as B vitamins appeared unevenly distributed among bacteria. Altogether, our results brought insights into the bacterial diversity found in diatom-bacterial communities and hinted at metabolic interdependencies within the community that could result in diatom-bacterial and bacterial-bacterial interactions. The present work allowed us to explore the functional architecture of the bacterial community associated with A. formosa in culture and is complementary to field studies.

Temporal variability of bacterioplankton is habitat driven

Temporal dynamics of bacterioplankton are rarely investigated for multiple habitats and years within individual lakes, limiting our understanding of the variability of bacterioplankton community (BC) composition with respect to environmental factors. We assessed the BC composition of a littoral and two pelagic habitats (euphotic zone and hypolimnion) of Lake Tovel monthly from April 2014 to May 2017 by high-throughput sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. The three habitats differed in temperature, light, oxygen and hydrology. In particular, the littoral was the most hydrologically unstable because it receives most of the lake inflow, the hypolimnion was the most stable because of its hydrologically sheltered position, and the pelagic euphotic habitat was intermediate. Consequently, we hypothesized different temporal patterns of BC composition for all three habitats according to their environmental differences. We applied PERMANOVA, nonmetric multidimensional scaling and source-sink analysis to characterize BC composition. Overall, BCs were different among habitats with the littoral showing the highest variability and the hypolimnion the highest stability. The BC of rainy 2014 was distinct from the BCs of other years irrespective of the habitats considered. Seasonal differences in BCs were limited to spring, probably linked to meltwater inflow and mixing. Thus, temporal effects related to year and season were linked to the hydrological gradient of habitats. We suggest that despite potential within-lake dispersal of bacterioplankton by water flow and mixing, local environmental conditions played a major role in Lake Tovel, fostering distinct BCs in the three habitats.

TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution

Taxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater data sets using the comprehensive SILVA database and the freshwater-specific FreshTrain database. TaxAss increased the percentage of the data set classified compared to using only SILVA, especially at fine-resolution family to species taxon levels, while across the freshwater test data sets classifications increased by as much as 11 to 40% of total reads. A similar increase in classifications was not observed in a control mouse gut data set, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxon levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxon levels, incorrect classifications became significant. We validated TaxAss using simulated amplicon data derived from full-length clone libraries and found that 96 to 99% of test sequences were correctly classified at fine resolution. TaxAss splits a data set's sequences into two groups based on their percent identity to reference sequences in the ecosystem-specific database. Sequences with high similarity to sequences in the ecosystem-specific database are classified using that database, and the others are classified using the comprehensive database. TaxAss is free and open source and is available at https://www.github.com/McMahonLab/TaxAssIMPORTANCE Microbial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or unique sequences. These fine-resolution groupings are more ecologically relevant, but OTU definitions are data set dependent and cannot be compared between data sets. Microbial ecologists studying freshwater have curated a small, ecosystem-specific taxonomy database to provide consistent and up-to-date terminology. We created TaxAss, a workflow that leverages this database to assign taxonomy. We found that TaxAss improves fine-resolution taxonomic classifications (family, genus, and species). Fine taxonomic groupings are more ecologically relevant, so they provide an alternative to OTU-based analyses that is consistent and comparable between data sets.

Unrevealing variation of microbial communities and correlation with environmental variables in a full culture-cycle of Undaria pinnatifida

Bacteria are the most abundant organisms in natural environment and dominant drivers of multiple geochemical functions. Drawing a global picture of microbial community structure and understanding their ecological status remain a grand challenge. As a typical artificial process, aquaculture provides a large amount of foods and creates great economic benefits for human beings. However, few studies are aimed at the microbial community in the aquaculture environment of aquatic plants. We analyzed microbial communities from 21 water samples in a coastal aquaculture area during the whole cultural process of Undaria pinnatifida by using high-throughout sequencing of 16S rRNA gene. The progression of U. pinnatifida aquaculture can be divided into three stages, named Seeding, Growth, and Maturity, respectively. Microbial community structures in water of the aquaculture area were significantly changed during the progression of U. pinnatifida aquaculture. The relative abundance of Flavobacteriia and Thaumarchaeota classes increased in Growth stage, and β-proteobacteria and Acidimirobiia classes decreased with the growth of U. pinnatifida. Meanwhile, environmental factors shaping the microbial community structures were uncovered during the U. pinnatifida aquaculture by using canonical correspondence analysis and Mantel test, in which temperature, dissolved oxygen, pH and nitrogen could be the major influencing factors. In addition, the microbial functions based on KEGG pathways were predicted from the microbial community compositions by PICRUSt. The comparison of predicted functions suggested that Environmental Information Processing and Genetic Information Processing were the functional categories with the most obvious shift in abundance among different stages of U. pinnatifida aquaculture. The findings of this study allowed us to better understand the microbial community in coastal aquaculture systems and the impact of seaweed cultivation on coastal ecosystems.

Interplay between gut microbiota metabolism and inflammation in HIV infection

HIV infection causes a disruption of gut-associated lymphoid tissue, driving a shift in the composition of gut microbiota. A deeper understanding of the metabolic changes and how they affect the interplay with the host is needed. Here, we assessed functional modifications of HIV-associated microbiota by combining metagenomic and metatranscriptomic analyses. The transcriptionally active microbiota was well-adapted to the inflamed environment, overexpressing pathways related to resistance to oxidative stress. Furthermore, gut inflammation was maintained by the Gram-negative nature of the HIV-associated microbiota and underexpression of anti-inflammatory processes, such as short chain fatty acid biosynthesis or indole production. We performed co-occurrence and metabolic network analyses that showed relevance in the microbiota structure of both taxonomic and metabolic HIV-associated biomarkers. The Bayesian network revealed the most determinant pathways for maintaining the structure stability of the bacterial community. In addition, we identified the taxa's contribution to metabolic activities and their interactions with host health.

Combining High-Throughput Sequencing of sedaDNA and Traditional Paleolimnological Techniques To Infer Historical Trends in Cyanobacterial Communities

Freshwaters worldwide are under increasing pressure from anthropogenic activities and changing climate. Unfortunately, many inland waters lack sufficient long-term monitoring to assess environmental trends. Analysis of sedimentary ancient DNA ( sedaDNA) is emerging as a means to reconstruct the past occurrence of microbial communities of inland waters. The purpose of this study was to assess a combination of high-throughput sequencing (16S rRNA) of sedaDNA and traditional paleolimnological analyses to explore multidecadal relationships among cyanobacterial community composition, the potential for cyanotoxin production, and paleoenvironmental proxies. DNA was extracted from two sediment cores collected from a northern Canadian Great Plains reservoir. Diversity indices illustrated significant community-level changes since reservoir formation. Furthermore, higher relative abundances in more recent years were observed for potentially toxic cyanobacterial genera including Dolichospermum. Correlation-based network analysis revealed this trend significantly and positively correlated to abundances of the microcystin synthetase gene ( mcyA) and other paleoproxies (nutrients, pigments, stanols, sterols, and certain diatom species), demonstrating synchrony between molecular and more standard proxies. These findings demonstrate a novel approach to infer long-term dynamics of cyanobacterial diversity in inland waters and highlight the power of high-throughput sequencing to reconstruct trends in environmental quality and inform lake and reservoir management and monitoring program design.

Synchrony of Eukaryotic and Prokaryotic Planktonic Communities in Three Seasonally Sampled Austrian Lakes

Freshwater systems are characterized by an enormous diversity of eukaryotic protists and prokaryotic taxa. The community structures in different lakes are thereby influenced by factors such as habitat size, lake chemistry, biotic interactions, and seasonality. In our study, we used high throughput 454 sequencing to study the diversity and temporal changes of prokaryotic and eukaryotic planktonic communities in three Austrian lakes during the ice-free season. In the following year, one lake was sampled again with a reduced set of sampling dates to observe reoccurring patterns. Cluster analyses (based on SSU V9 (eukaryotic) and V4 (prokaryotic) OTU composition) grouped samples according to their origin followed by separation into seasonal clusters, indicating that each lake has a unique signature based on OTU composition. These results suggest a strong habitat-specificity of microbial communities and in particular of community patterns at the OTU level. A comparison of the prokaryotic and eukaryotic datasets via co-inertia analysis (CIA) showed a consistent clustering of prokaryotic and eukaryotic samples, probably reacting to the same environmental forces (e.g., pH, conductivity). In addition, the shifts in eukaryotic and bacterioplanktonic communities generally occurred at the same time and on the same scale. Regression analyses revealed a linear relationship between an increase in Bray-Curtis dissimilarities and elapsed time. Our study shows a pronounced coupling between bacteria and eukaryotes in seasonal samplings of the three analyzed lakes. However, our temporal resolution (biweekly sampling) and data on abiotic factors were insufficient to determine if this was caused by direct biotic interactions or by reacting to the same seasonally changing environmental forces.

Bioaugmentation of chlorothalonil-contaminated soil with hydrolytically or reductively dehalogenating strain and its effect on soil microbial community

Although bioaugmentation of pollutant-contaminated sites is a great concern, there are few reports on the relationships among indigenous microbial consortia, exogenous inocula, and pollutants in a bioaugmentation process. In this study, bioaugmentation with Pseudochrobactrum sp. BSQ1 and Massilia sp. BLM18, which can hydrolytically and reductively dehalogenate chlorothalonil (TPN), respectively, was studied for its ability to remove TPN from soil; the alteration of the soil microbial community during the bioaugmentation process was investigated. The results showed that TPN (50 mg/kg) was completely removed in both bioaugmentation treatments within 35 days with half-lives of 6.8 and 9.8 days for strains BSQ1 and BLM18 respectively. In high concentration of TPN-treated soils (100 mg/kg), the bioaugmentation with strains BSQ1 and BLM18 respectively reduced 76.7% and 62.0% of TPN within 35 days. The TPN treatment significantly decreased bacterial richness and diversity and improved the growth of bacteria related to the elimination of chlorinated organic pollutants. However, little influence on soil microbial community was observed for each inoculation treatment (without TPN treatment), showing that TPN treatment is the main force for the shift in indigenous consortia. This study provides insights into the effects of halogenated fungicide application and bioaugmentation on indigenous soil microbiomes.

Ecological Patterns Among Bacteria and Microbial Eukaryotes Derived from Network Analyses in a Low-Salinity Lake

Microbial communities are comprised of complex assemblages of highly interactive taxa. We employed network analyses to identify and describe microbial interactions and co-occurrence patterns between microbial eukaryotes and bacteria at two locations within a low salinity (0.5-3.5 ppt) lake over an annual cycle. We previously documented that the microbial diversity and community composition within Lake Texoma, southwest USA, were significantly affected by both seasonal forces and a site-specific bloom of the harmful alga, Prymnesium parvum. We used network analyses to answer ecological questions involving both the bacterial and microbial eukaryotic datasets and to infer ecological relationships within the microbial communities. Patterns of connectivity at both locations reflected the seasonality of the lake including a large rain disturbance in May, while a comparison of the communities between locations revealed a localized response to the algal bloom. A network built from shared nodes (microbial operational taxonomic units and environmental variables) and correlations identified conserved associations at both locations within the lake. Using network analyses, we were able to detect disturbance events, characterize the ecological extent of a harmful algal bloom, and infer ecological relationships not apparent from diversity statistics alone.