Distinct Community Structure Research Articles

Cross-correlation dynamics and community structures of cryptocurrencies

Cryptocurrencies have become a prominent investment tool recently with increasing interest in them and their relationships with stock and foreign exchange markets. We analyze here the cross-correlations of price changes of different cryptocurrencies using Random Matrix Theory and extract community structures by constructing minimum spanning trees, finding their eigenvalues contrast sharply with universal predictions of Random Matrix Theory. We reveal distinct transient community structures among different groupings of cryptocurrencies. By studying the cross-correlation dynamics of sub-communities we find evidence of collective behaviour. Furthermore, we compare eigenvalue changes and find prominent groupings following a community trend, useful for creating cryptocurrency portfolios.

An altered fecal microbial profiling in rosacea patients compared to matched controls

Rosacea has been linked to inflammatory bowel disease and small bowel bacterial overgrowth. We aimed to investigate the fecal microbial profiling and the potential gene functions between rosacea and non-rosacea subjects. A case-control study. Fecal microbiome and predicted genetic function inferred from high-throughput 16S ribosomal RNA sequencing were analyzed between rosacea (n = 11) and age-, gender- and body mass index-matched non-rosacea subjects (n=110). The correlation between altered microbiome as well as lifestyle and diet were also investigated. A significant reduction of fecal microbial richness was found in rosacea patients. A distinct fecal microbial community structure was demonstrated in rosacea patients. The discriminating enriched genera in rosacea patients included Rhabdochlamydia, CF231, Bifidobacterium, Sarcina, Ruminococcus, belonging to the phylum of Chlamydiae, Bacteroidetes, Actinobacteria, and Lentisphaerae. The discriminating reduced abundant genera included Lactobacillus, Megasphaerae, Acidaminococcus, Hemophilus, Roseburia, Clostridium, belong to the phylum of Firmicutes; and Citrobacter, belonging to the phylum of Proteobacteria. The distinct fecal microbial composition might be related to sulfur metabolism, cobalamin, and carbohydrate transport. An altered fecal microbial richness and composition were observed in rosacea patients. The distinct microbial composition might be related to sulfur metabolism, cobalamin and carbohydrate transport.

Palmitic acid accumulation limits methane production in anaerobic co-digestion of fats, oils and grease with municipal wastewater sludge

Anaerobic co-digestion of fats, oils and grease (FOG) with municipal wastewater sludge offers the opportunity to increase methane yields; yet the impact of FOG on overall process dynamics and the associated microbial communities is not well understood. This study employed lab-scale batch anaerobic co-digestion assays to advance the understanding of the co-digestion process through studying the dynamics of formation and consumption of intermediates along the anaerobic digestion pathway and correlating these to temporal analysis of methanogenic activity as well as end-point microbial community structure. Methane production was delayed during sludge co-digestion with FOG, but not during digestion of sludge alone. Palmitic acid, a long-chain fatty acid (LCFA), accumulated during co-digestion to concentrations above 16 mM, resulting in a lag in methane production. Acetate, hydrogen, and formate, carbon and/or energy sources for methanogens during methane production, did not accumulate during the lag-phase. Expression of the mcrA gene, which encodes the methyl coenzyme M reductase alpha subunit necessary for catalyzing the final step of methanogenesis, increased when co-digesters were spiked with acetate during the lag-phase, indicating no direct total inhibition from palmitic acid to methanogenic activity in assays with a 23% FOG loading (based on total g VS). End-point microbial community analyses revealed distinct community structure and composition differences between co-digestion assays and controls, and between biological replicates with variable responses. The hydrogenotrophic methanogen genus Methanoculleus dominated adapted co-digesters, but not inhibited co-digesters suggesting its importance for adapting to FOG loadings. Palmitic acid accumulation resulting from distinct microbial community composition and structure thus characterizes stalled or inhibited FOG co-digesters.

Human-engineered hydrodynamic regimes as a driver of cryptic microinvertebrate assemblages on urban artificial shorelines

Urban shorelines undergo substantial hydrodynamic changes as a result of coastal engineering and shoreline armouring that can alter sedimentation, turbidity, and other factors. These changes often coincide with major shifts in the composition and distribution of marine biota, however, rarely are hydrodynamic-mediated factors confirmed experimentally as the mechanism underpinning these shifts. This study first characterized hydrodynamic-related distribution patterns among epilithic and epiphytic microinvertebrates on urban seawalls in Singapore. We found reduced microinvertebrate abundances and distinct microinvertebrate community structure within benthic turf algae in areas where coastal defences had reduced wave energy and increased sediment deposition, among other hydrodynamic-related abiotic changes. Low-exposure areas also had reduced densities of macroinvertebrate grazers and less dense turf algae (lower mass per cm2) than adjacent high-exposure areas. Using harpacticoid copepods as a model taxon, we performed a reciprocal transplant experiment to discern between the effects of exposure-related conditions and grazing. Results from the experiment indicate that conditions associated with restricted wave energy from shoreline engineering limit harpacticoid population densities, as transplantation to low-exposure areas led to rapid reductions in abundance. At the same time, we found no effect from grazer exclusion cages, suggesting harpacticoids are minimally impacted by exposure-related gradients in gastropod macrograzer densities over short time scales. Given the key role of intertidal microinvertebrates, particularly harpacticoids, in nearshore food webs, we postulate that human-engineered hydrodynamic regimes are an important factor shaping marine ecosystem functioning in urban areas.

Spatial variation of bacterial and fungal communities of estuarine seagrass leaf microbiomes

The health of seagrass plants, and thereby the ecosystems they form, is linked to their associated microbial communities. However, the role of the microbiome in holobiont function and health remains poorly understood for most seagrass species and environmental pressures, and there is, therefore, a need to better understand the drivers behind the formation of and external influences on the seagrass microbiome. Using a core microbiome framework, we characterised the leaf microbiomes of 6 estuarine seagrass populations after a precipitation event to explore how the microbiomes vary across different sites and salinities over a regional spatial scale. We found that each estuary had distinct core bacterial community structures (beta-diversity), but shared a more similar fungal core community structure. We hypothesise that the differences in the bacterial members of the microbiomes among estuaries are generally the result of each estuary being influenced by unique watersheds and sources of prokaryotes. In contrast, the similarity in the core fungal communities suggests that the eukaryotic components of the microbiomes are likely under selection or result from similar colonisation pathway(s). We also found that the bacterial taxa driving the differences among estuaries were linked to the salinity of the estuary, likely due to (1) the general epibiotic nature of colonisation (i.e. watershed source and exposure) and (2) members or functional groups within the leaf microbiome assisting seagrasses in coping with the extreme salinities. These results are valuable for linking microbiomes to the resilience of seagrasses living within dynamic estuaries experiencing a range of physicochemical pressures.

Shifts in the bacterial community of saliva give insights on the relationship between obesity and oral microbiota in adolescents.

The current study aimed at the determination of the impact of obesity on the salivary microbiome in adolescents. Sixty subjects ranging 14-17years old were enrolled (obese: n = 30-50% females, and normal weight: n = 30-50% females). Stimulated saliva was collected for denaturing gradient gel electrophoresis (DGGE) band patterns and massive 16S rRNA gene sequencing using the Ion Torrent platform. Overall, data analysis revealed that male subjects harbored a higher diverse salivary microbiome, defined by a significant higher richness (32.48 versus 26.74) and diversity (3.36 versus 3.20), higher Simpson values (0.96 versus 0.95) and distinct bacterial community structure considering either sex or condition (p < 0.05). Bacterial community fingerprinting analysis in human saliva showed a positive correlation with increased body mass index (BMI) in adolescents. Veillonella, Haemophilus and Prevotella occurrence was found to be affected by BMI, whereas Neisseria and Rothia occurrence was significantly impacted by sex in obese subjects. Our findings suggest that male and female adolescents may harbor a naturally distinct salivary microbiota and that obesity may specifically have an impact on their oral bacterial community. The potential dysbiotic oral microbiome in obese adolescents raises new insights on the etiology and prevention of future conditions in these populations.

The Root Nodule Microbiome of Cultivated and Wild Halophytic Legumes Showed Similar Diversity but Distinct Community Structure in Yellow River Delta Saline Soils.

Symbiotic associations between leguminous plants and their nodule microbiome play a key role in sustainable agriculture by facilitating the fixation of atmospheric nitrogen and enhancing plant stress resistance. This study aimed to decipher the root nodule microbiome of two halophytic legumes, Sesbania cannabina and Glycine soja, which grow in saline soils of the Yellow River Delta, China, using PacBio’s circular consensus sequencing for full-length bacterial 16S rRNA gene to obtain finer taxonomic information. The cultivated legume Glycine max was used for comparison. We identified 18 bacterial genera and 55 species in nodule samples, which mainly classified to Proteobacteria, and rhizobial genus Ensifer was the predominant group. The three legumes showed similarity in operational taxonomic unit (OTU) diversity but distinction in OTU richness, indicating that they harbor similar bacterial species with different relative contents. The results of principal coordinates analysis and ANOSIM tests indicated that G. soja and G. max have similar nodule bacterial communities, and these communities differ from that of S. cannabina. Wild legumes S. cannabina and G. soja both harbored a higher number of rhizobia, while G. max possessed more non-rhizobial bacteria. These differences could be associated with their adaptability to saline–alkali stress and revealed clues on the nodule endophytes with relative importance of culturable rhizobial symbionts.

Differences in bacterial community structure and potential functions among Eucalyptus plantations with different ages and species of trees

Bacteria are the most abundant microbes in soil and play an important role in the carbon and nitrogen cycles. Currently, China has become the country with the second largest Eucalyptus planting area. However, the dynamic changes in the soil bacterial community in different Eucalyptus plantations has been poorly studied. In the present study, the bacterial community structure and potential function associated with Eucalyptus plantations of different ages (1- and 5+-year) and species (E. urophylla × E. grandis, E. camaldulens and E. pellita) in Zhanjiang, Guangdong Province, China were characterized using Illumina MiSeq. technology coupled with Functional Annotation of Prokaryotic Taxa (FAPROTAX) analysis. The results showed that the bacterial diversity increased with increasing plantation age, with different ages and species of trees forming distinct bacterial community and functional structures, respectively (P < 0.05 in all possible pairs). The most abundant phyla across all samples were Actinobacteria (35.9% of total sequences), Proteobacteria (20.5%), Chloroflexi (10.3%) and Acidobacteria (9.2%). With increasing plantation age, the bacterial community shifted from the phylum WPS-2 and order Sphingomonadales as dominant taxa to the order GP6. The community function also changed from carbon utilization to more nitrogen and sulfur cycling processes. The soil pH, organic carbon, water content and total nitrogen were identified as the key factors affecting both community structure and function. The results indicate that Eucalyptus plantation age has a greater effect on the bacterial community diversity and structure than Eucalyptus species. This study provides useful information on the importance of microbes for the sustainable management of Eucalyptus plantations in the future.

Anaerobic digestion of co-ensiled cover crop and barley straw: Effect of co-ensiling ratios, manure addition and impact on microbial community structure

Cover cropping is important for nutrient management of agricultural systems and has largely unexploited potential for biogas production. Co-harvest of cover crops and straw and storage as silage blends prior to biogas is promising as it could enhance the long-term storability and lead to synergies for anaerobic digestion. However, it is necessary to evaluate the feasibility of using co-ensiled blends and process optimization based on continuous test. In this study, semi-continuous thermophilic anaerobic digestion experiments were carried out with feeding of cover crop silage, co-ensiled cover crop and straw (with mixing ratios in relation to various harvest strategies) with or without addition of cattle manure. The main objective is to determine the feasibility of aforementioned mixtures for biogas production and the influence on microbial community structures in response to various feeding compositions. Results demonstrated that cover crop (silage) is feasible for digestion alone or with addition of barley straw, cattle manure or both, while manure addition led to higher CH4 yield/buffer capacity, and enhanced the volatile solids reduction. Microbial community compositions were found to have been affected by the feeding, while high straw addition led to a distinct community structure.

Community structure of Anaeromyxobacter in Fe(III) reducing enriched cultures of paddy soils

Anaeromyxobacter is a typical representative genus of dissimilatory metal-reducing microbes. However, the community structure and metabolic function of Anaeromyxobacter have rarely been reported because of the limited number of Anaeromyxobacter isolations. Therefore, this study aimed to investigate the community structure and succession of Anaeromyxobacter in a Fe(III)-reducing enriched culture of paddy soils. A 40-day anaerobic incubation of paddy soils enriched with ferrihydrite and goethite was conducted to investigate the response of the community structure and succession of Anaeromyxobacter to iron oxide addition. The dominant Anaeromyxobacter in paddy soils were potentially capable of Fe(III) reduction. Ferrihydrite enrichment increased the absolute abundance of Anaeromyxobacter by 0.01 × 108 to 3.2 × 108 copies g−1 soil, while goethite enrichment increased the absolute abundance of Anaeromyxobacter by 0.004 × 108 to 1.8 × 108 copies g−1 soil. Iron oxide enrichment significantly influenced the richness of Anaeromyxobacter during the later stages of incubation but had a negligible influence on the evenness. Nonetheless, Fe(II) accumulation was stimulated by ferrihydrite enrichment after paddy soil was incubated for 5 days, whereas goethite had a negligible effect on Fe(II) accumulation. Redundancy analysis revealed that Anaeromyxobacter community succession was closely correlated with the processes of Fe(III) reduction. Exogenous ferrihydrite addition showed a greater influence than goethite on the Anaeromyxobacter community during anaerobic incubation of paddy soils. The difference in inherent amorphous iron oxide content in paddy soils was also decisive in the distinct community structure and succession of Anaeromyxobacter in paddy soils.

Silver nanoparticle and Ag+-induced shifts of microbial communities in natural brackish waters: Are they more pronounced under oxic conditions than anoxic conditions?

With the burst of silver nanoparticles (AgNPs) applications, their potential entry into the environment has attracted increasing concern. To date, researches about the impacts of AgNPs on microbial communities have been scarcely conducted in the brackish waters. Here, the effects of interactions of AgNPs and Ag+ (as a positive control) with dissolved oxygen on natural brackish water microbial communities were investigated for 30 d. The introduction of AgNPs and Ag+ in natural brackish waters resulted in distinct bacterial community composition and structure as well as reduction of the richness and diversity, effects that were not eliminated completely during the tested periods. Anoxic conditions could attenuate the effects of AgNPs and Ag+ on the community, and dissolved oxygen made more contributions to community compositions for short-term exposure. High doses of AgNPs had more pronounced long-term impacts than Ag+ amendment. Compared with the controls, two general AgNP and Ag+ responses, namely, sensitivity and resistance, were observed. Sensitive species mainly included those of the genera Synechococcus and unclassified_f_Rhodobacteraceae, while resistant species mostly belonged to the phylum Bacteroidetes and participated in carbon metabolic processes. Our results indicated that the microbial communities that were involved in nutrient cycles (such as carbon, nitrogen, and sulfide) and photoautotrophic bacteria that contained bacteriochlorophyll were adversely affected by AgNPs and Ag+. In addition, dissolved oxygen could further change the microbial communities. These results implied that under different oxygen conditions AgNPs possibly resulted in varying microbial survival strategies and affected the biogeochemical cycling of nutrients in natural brackish waters.

Trophic Status Is Associated With Community Structure and Metabolic Potential of Planktonic Microbiota in Plateau Lakes.

Microbes in various aquatic ecosystems play a key role in global energy fluxes and biogeochemical processes. However, the detailed patterns on the functional structure and the metabolic potential of microbial communities in freshwater lakes with different trophic status remain to be understood. We employed a metagenomics workflow to analyze the correlations between trophic status and planktonic microbiota in freshwater lakes on Yun-Gui Plateau, China. Our results revealed that microbial communities in the eutrophic and mesotrophic-oligotrophic lake ecosystems harbor distinct community structure and metabolic potential. Cyanobacteria were dominant in the eutrophic ecosystems, mainly driving the processes of aerobic respiration, fermentation, nitrogen assimilation, nitrogen mineralization, assimilatory sulfate reduction and sulfur mineralization in this ecosystem group. Actinobacteria, Proteobacteria (Alpha-, Beta-, and Gammaproteobacteria), Verrucomicrobia and Planctomycetes, occurred more often in the mesotrophic-oligotrophic ecosystems than those in the eutrophic ecosystems, and these taxa potentially mediate the above metabolic processes. In these two groups of ecosystems, a difference in the abundance of functional genes involved in carbohydrate metabolism, energy metabolism, glycan biosynthesis and metabolism, and metabolism of cofactors and vitamins significantly contribute to the distinct functional structure of microbiota from surface water. Furthermore, the microbe-mediated metabolic potentials for carbon, nitrogen and sulfur transformation showed differences in the two ecosystem groups. Compared with the mesotrophic-oligotrophic ecosystems, planktonic microbial communities in the eutrophic ecosystems showed higher potential for aerobic carbon fixation, fermentation, methanogenesis, anammox, denitrification, and sulfur mineralization, but they showed lower potential for aerobic respiration, CO oxidation, nitrogen fixation, and assimilatory sulfate reduction. This study offers insights into the relationships of trophic status to planktonic microbial community structure and its metabolic potential, and identifies the main taxa responsible for the biogeochemical cycles of carbon, nitrogen and sulfur in freshwater lake environments.

Ammonia Oxidizers in High-Elevation Rivers of the Qinghai-Tibet Plateau Display Distinctive Distribution Patterns.

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) as well as comammox catalyze ammonia oxidation. The distribution and biogeography of these ammonia oxidizers might be distinctive in high-elevation rivers, which are generally characterized by low temperature and low ammonium concentration but strong solar radiation; however, these characteristics have rarely been documented. This study explored the abundance, community, and activity of ammonia oxidizers in the overlying water of five rivers in the Qinghai-Tibet Plateau (QTP). Potential nitrification rates in these rivers ranged from 5.4 to 38.4 nmol N liter-1 h-1, and they were significantly correlated with ammonium concentration rather than temperature. Comammox were found in 25 of the total 28 samples, and they outnumbered AOA in three samples. Contrary to most studied low-elevation rivers, average AOB amoA gene abundance was significantly higher than that of AOA, and AOB/AOA ratios increased with decreasing water temperature. The Simpson index of the AOA community increased with elevation (P < 0.05), and AOA and AOB communities exhibited high dissimilarities with low-elevation rivers. Cold-adapted (Nitrosospira amoA cluster 1, 33.6%) and oligotrophic (Nitrosomonas amoA cluster 6a, 31.7%) groups accounted for large proportions in the AOB community. Suspended sediment concentration exerted significant effects on ammonia oxidizer abundance (r > 0.56), and owing to their elevational variations in source and concentration, suspended sediments facilitated distance-decay patterns for AOA and AOB community similarities. This study demonstrates distinctive biogeography and distribution patterns for ammonia oxidizers in high-elevation rivers of the QTP. Extensive research should be conducted to explore the role of these microbes in the nitrogen cycle of this zone.IMPORTANCE Ammonia-oxidizing archaea (AOA) and bacteria (AOB) as well as comammox contribute to ammonia oxidation, which plays significant roles in riverine nitrogen cycle and N2O production. Source regions of numerous rivers in the world lie in high-elevation zones, but the abundance, community, and activity of ammonia oxidizers in rivers in high-elevation regions have rarely been investigated. This study revealed distinctive distribution patterns and community structures for ammonia oxidizers in five high-elevation rivers of the Qinghai-Tibet Plateau, and the individual and combined effects of low temperature, low nutrients, and strong solar radiation on ammonia oxidizers were elucidated. The findings of this study are helpful to broaden our knowledge on the biogeography and distribution pattern of ammonia oxidizers in river systems. Moreover, this study provides some implications to predict the performance of ammonia oxidizers in high-elevation rivers and its variations under global climate warming.

496 Baseline and Longitudinal Microbial Changes Predict Response to Rifaximin and/or Diet Low in Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols in Irritable Bowel Syndrome

INTRODUCTION: Diarrhea-predominant irritable bowel syndrome (IBS-D) is a chronic, disabling condition. Treatments for IBS-D, including rifaximin, a nonabsorbable antibiotic, and a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP), improve symptoms in ≤50% of patients. We hypothesized that changes in the gut microbiota predict response to treatment for IBS-D. METHODS: We randomized 17 patients meeting Rome IV criteria for IBS-D to receive either rifaximin 550 mg three times daily x 14 days or a low FODMAP diet x 4 wks. The primary outcome was proportion of responders to intervention defined by ≥30% improvement in mean daily abdominal pain or bloating scores. The secondary outcome was ≥50-point decrease in IBS-Severity Symptom Scoring (IBS-SSS) compared with baseline. Fecal samples were collected at baseline and 2, 4 and 5 wks. The microbial community in these specimens was characterized by 16S rRNA encoding-gene sequence analysis. RESULTS: There were 6 subjects (60.0%) in the rifaximin group and 4 subjects (57.1%) in the low FODMAP group that met the primary endpoint (P &gt; .99) (Table 1). Patients in the rifaximin group had significant improvements in abdominal pain (P = .01), bloating (P = .02), and IBS-SSS (P = .009) compared with baseline. Patients in the low FODMAP group showed improvement in IBS-SSS only (P = .06) at the end of treatment. Responders to treatment had unique inter- and intra-individual temporal characteristics compared with non-responders. Responders to rifaximin and low FODMAP diet showed a distinct microbial community structure at baseline compared with non-responders (P = .001 for both, Figure 1A). Responders to rifaximin (P = .08) and low FODMAP diet (P = .01) also exhibited lower degrees of microbial community change during therapy compared with non-responders (Figure 1B). Responders to rifaximin (Figure 2A) and low FODMAP diet (Figure 2B) showed changes in several taxa at baseline and longitudinally compared with non-responders. CONCLUSION: Responders to therapy with rifaximin and low FODMAP diet show a distinct fecal microbial community structure at baseline. Many microbiome features at baseline predict response to treatment. Longitudinal analyses show responders have a more resilient community structure to either rifaximin or dietary modification compared with non-responders. The functional significance of these microbial changes in responders vs. non-responders is unclear, but may be the focus of future studies.

Integrated Space-Time Dataset Reveals High Diversity and Distinct Community Structure of Ciliates in Mesopelagic Waters of the Northern South China Sea.

Little is known about diversity distribution and community structure of ciliates in mesopelagic waters, especially how they are related to spatial and temporal changes. Here, an integrative approach, combining high-throughput cDNA sequencing and quantitative protargol stain, was used to analyze ciliate communities collected temporally along a transect from coastal to oceanic regions at depths ranging from the surface to 1000 m. The mesopelagic zone exhibited comparable alpha diversity to surface water which was consistent over temporal variation, with high diversity occurring at the interface with the euphotic zone. Comparison with the northeastern and the western Pacific Ocean revealed consistency of this vertical distribution of ciliates across oceanic basins. Mesopelagic ciliates harbored distinct community structure without significant seasonal differences, with the vertical variations driven largely by members of the classes Spirotrichea and Oligohymenophorea. Operational taxonomic units (OTUs) affiliated with Scuticociliatia, Astomatida and Apostomatida, members of which are known to be bacterivorous and/or commensal/parasitic species, were more abundant in mesopelagic waters than above, implying they are an important component of food webs in the mesopelagic zone. A combination of depth, geographic distance and environment shaped the ciliate communities, with depth being the most influential factor. Phylogenetic null modeling analysis further indicated that 57.1 and 33.3% of mesopelagic community variation was governed by dispersal limitation and heterogeneous selection, respectively, probably due to the marked biochemical and physical gradients down the water column. This suggests that ciliate community structure in the mesopelagic zone is mainly controlled by stochastic processes. Collectively, this study reports mesopelagic ciliates exhibited high diversity and distinct community structure across spatiotemporal scales and informs the processes mediating ciliate assembly in the mesopelagic zone. These should be fully considered in future studies to build a more comprehensive understanding of mesopelagic microbial assemblages.

Seasonal dynamics of cyanobacteria and eukaryotic phytoplankton in a multiple-reservoir recycling irrigation system

BackgroundAgricultural runoff recycling systems are manmade aquatic ecosystems of growing significance to global water sustainability, crop health, and production. This study investigated the seasonal dynamics of microbial community in a three-reservoir recycling irrigation system with a stepwise water flow and compared with that of an adjacent runoff-free stream. Runoff water from all production areas was captured in a sedimentation reservoir which overflowed to a transition reservoir then retention reservoir through a culvert. Stream water was pumped to replenish the reservoirs as needed during growing seasons.Results16S rDNA PCR clone libraries of quarterly water samples from three reservoirs and one stream were sequenced, and 575 operational taxonomic units (OTUs) were identified and assigned to cyanobacteria, eukaryotic phytoplankton, and other bacteria. When compared to the stream, three reservoirs consistently had low microbial diversity. A distinct seasonal pattern of microbial community structure was observed for each reservoir and the stream. Stream was consistently dominated by other bacteria. Retention reservoir was dominated by cyanobacteria during the summer and fall and eukaryotic phytoplankton during the winter and spring. Sedimentation reservoir was dominated by cyanobacteria beginning in the spring but that dominance was altered when water was pumped from the stream from early spring to fall seasons. Transition reservoir had the greatest shift of microbial community structure, being dominated by other bacteria in the summer, cyanobacteria in the fall, and eukaryotic phytoplankton in the winter and spring. Water temperature and ammonium level were the two most important contributing factors to the seasonality of microbial community in these reservoirs.ConclusionsThe three recycling irrigation reservoirs consistently had lower microbial diversity and distinct community structure when compared to the stream. These reservoirs were typically dominated by cyanobacteria during warm seasons and eukaryotic phytoplankton during cool seasons. This seasonal pattern was altered when water was pumped from the stream. The cyanobacteria dominance was associated with rising water temperature and ammonium level. These results highlight the importance of preventing agricultural runoff from entering natural waterways and water resources and provide a useful framework for further investigations into the ecological processes of this emerging ecosystem.

Biodegradation of petroleum hydrocarbons and changes in microbial community structure in sediment under nitrate-, ferric-, sulfate-reducing and methanogenic conditions

In the present study, the biodegradation behaviors of petroleum hydrocarbons under various reducing conditions were investigated. n-Alkanes and polycyclic aromatic hydrocarbons (PAHs) were degraded with NO3−, Fe3+, SO42−, or HCO3− as terminal electron acceptors (TEAs), which link to four typical reducing conditions (i.e., nitrate-reducing, ferric-reducing, sulfate-reducing and methanogenic conditions, respectively) in sediment. The fastest degradation rates were achieved under sulfate-reducing conditions with half-lives of 49.51 days for n-alkanes and 58.74 days for PAHs. For short-chain n-alkanes and low-molecular weight (LMW) PAHs, relatively higher removal efficiencies were achieved under nitrate- and ferric-reducing conditions. The degradation of long-chain n-alkanes and high-molecular weight (HMW) PAHs coupled to methanogenesis was the most favored as compared with other reducing conditions. Carboxylation was found to be the principle mechanism for regulating n-alkane degradation coupled to denitrification, while the activation of n-alkanes by the addition of fumarate was the principle mechanism for the n-alkane degradation under sulfate-reducing conditions. The anaerobic metabolism of n-alkanes may not proceed via fumarate addition or carboxylation under ferric-reducing and methanogenic conditions. Illumina HiSeq sequencing revealed dissimilar structures of the microbial communities under various reducing conditions. It is hypothesized that the utilization of different TEAs for n-alkane and PAH degradation resulted in distinct microbial community structures, which were highly correlated with the varied degradation behaviors of petroleum hydrocarbons in sediment. The current results may provide reference value on better understanding the biodegradation behaviors of n-alkanes and PAHs in association with the induced microbial communities in sedimentary environments under the four typical reducing conditions.

Selective enrichment of bacterial pathogens by microplastic biofilm

Microplastics have been found to be ubiquitous in freshwater ecosystems, providing a novel substrate for biofilm formation. Here, we incubated biofilm on microplastics and two natural substrates (rock and leaf) under a controlled environment to investigate the differences of microbial community structure, antibiotic resistance gene (ARG) profiles, and ARG microbial hosts between biofilms on three types of substrates. Results from high-throughput sequencing of 16S rRNA gene revealed that microplastic biofilm had a distinctive community structure. Network analyses suggested that microplastic biofilm possessed the highest node connected community, but with lower average path length, network diameter and modularity compared with biofilm on two natural particles. Metagenomic analyses further revealed microplastic biofilm with broad-spectrum and distinctive resistome. Specifically, according to taxonomic annotation of ARG microbial hosts, two opportunisitic human pathogens (Pseudomonas monteilii, Pseudomonas mendocina) and one plant pathogen (Pseudomonas syringae) were detected only in the microplastic biofilm, but not in biofilms formed on natural substrates. Our findings suggest that microplastic is a novel microbial niche and may serve as a vector for ARGs and pathogens to new environment in river water, generating freshwater environmental risk and exerting adverse impacts on human health.

LDPE microplastic films alter microbial community composition and enzymatic activities in soil

Concerns regarding microplastic contamination have spread from aquatic environments to terrestrial systems with a growing number of studies have been reported. Notwithstanding, the potential effects on soil ecosystems remain largely unexplored. In this study, the effects of polyethylene microplastics on soil enzymatic activities and the bacterial community were evaluated, and the microbiota colonizing on microplastics were also investigated. Microplastic amendment (2000 fragments per kg soil) significantly increased the urease and catalase activities in soil after 15 days, and no discernible alteration of invertase activities was detected. Results from high-throughput sequencing of 16S rRNA revealed that the alpha diversities (richness, evenness, and diversity) of the microbiota in soil were not obviously changed by the PE amendment, whereas the diversity indexes of microbiota on plastic fragments were significantly lower than those in the control and amended soils. Different taxonomic composition was observed in between the control and amended soils after 90 days of incubation. Bacterial assemblages with distinct community structure colonized the PE microplastics. Additionally, several taxa including plastic-degrading bacteria and pathogens were more abundant on microplastics. Simultaneously, the predicted functional profiles showed that the pathways of amino acid metabolism and xenobiotics biodegradation and metabolism were higher on the microplastics. These results indicated that microplastics in soil, compared with those in aquatic environments, can also act as a distinct microbial habitat, potentially altering the ecological functions of soil ecosystems.

New insights into the metagenomic link between pre‐treatment method, addition of an inoculum and biomethane yield during anaerobic digestion of water hyacinth (Eichhornia crassipes)

AbstractBACKGROUNDWater hyacinth (Eichhornia crassipes) is a fast growing water weed that threatens the aquatic ecosystem and human activities, hence control of the plant is essential. One such control approach is to harvest and utilize hyacinth as a substrate for anaerobic digestion (AD). Various factors influence AD performance, including substrate pre‐treatment and microbial community composition, amongst others. This study was aimed at establishing the link between method of substrate pre‐treatment, microbial diversity, inoculum addition and biogas yield during AD of hyacinth.RESULTSThe addition of an inoculum resulted in microbial community stability and early biomethane production of up to 0.4 L irrespective of pre‐treatment method. However, cultures that lacked inoculum showed distinct microbial community structure variation in response to pre‐treatment method, and minimal early biomethane production (up to 0.1 L). Biogas produced by cultures lacking inoculum was initially mostly composed of carbon dioxide (up to 100% of total biogas), but as digestion proceeded, an increase in biomethane production was observed (up to 60% of total biogas), which correlated with the shift in microbial community structure and increased microbial diversity. This indicates the presence of biogas‐producing microorganisms associated with the collected hyacinth. Canonical correspondence analysis proved that dynamic changes in microbial community structure and biogas yield were strongly correlative.CONCLUSIONThis study proves that hyacinth pre‐treatment influences microbial community structure and concomitant biogas yield in the absence of an inoculum. The addition of an inoculum aids in stability of microbial community structure and biogas yield irrespective of method of hyacinth pre‐treatment. © 2019 Society of Chemical Industry