Members Of Microbial Community Research Articles

Distinct Microbial Community of Phyllosphere Associated with Five Tropical Plants on Yongxing Island, South China Sea.

The surfaces of a leaf are unique and wide habitats for a microbial community. These microorganisms play a key role in plant growth and adaptation to adverse conditions, such as producing growth factors to promote plant growth and inhibiting pathogens to protect host plants. The composition of microbial communities very greatly amongst different plant species, yet there is little data on the composition of the microbiome of the host plants on the coral island in the South China Sea. In this study, we investigated the abundances and members of a major microbial community (fungi, bacteria, and diazotrophs) on the leaves of five dominant plant species (Ipomoea pes-caprae, Wedelia chinensis, Scaevola sericea, Cocos nucifera, and Sesuvium portulacastrum) on the island using real-time quantitative polymerase chain reaction (PCR) and high-throughput amplicon sequencing. Quantitative PCR results showed that fungi and bacteria were ubiquitous and variable among different host plants. Scaevola sericea showed the lowest absolute abundance and highest diversity of fungi and bacteria, while Cocos nucifera had the lowest abundance and the highest diversity of diazotrophs compare to the other four plants. There was a small proportion of shared microorganisms among the five different plants, while unique fungi, bacteria and diazotrophs were significantly enriched for different host plant species in this study (p < 0.05). Some of the most abundant organisms found in the communities of these different host plants are involved in important biogeochemical cycles that can benefit their host, including carbon and nitrogen cycles.

Sandy soils amended with bentonite induced changes in soil microbiota and fungistasis in maize fields

The addition of bentonite, used as soil conditioner, can promote sandy soil macro-aggregate formation, moisture content retention and increase soil nutrient concentrations. However, there is limited knowledge about how bentonite influences soil microbial communities and interconnections among community members associated with crops, such as maize in continuous production on sandy soils. Metabarcoding analysis of the fungal internal transcribed spacer 1 (ITS1) region and the bacterial 16S rRNA gene V4 region revealed that the fungal communities in sandy maize fields (dominated by Guehomyces, Alternaria and Mortierella) were more diverse and abundant in soils amended with bentonite than those without bentonite amendment. By contrast, the bacterial communities (dominated by Proteobacteria and Actinobacteria) had similar alpha-diversity under both conditions but many functional guilds, including those affiliated with fermentation and N-cycling, differed significantly in community compositional structure between soils with and without bentonite amendment. The increase in soil nutrient concentrations due to the addition of bentonite was a key factor associated with changes in the bacterial communities. However, the fungal communities were more strongly influenced by the capacity of bentonite to increase soil moisture retention and enhance macro-aggregate development. Molecular ecological network analysis revealed more competitive (62.1% of total significant associations) than cooperative (37.9%) associations among microbial community members across all soils studied. The observation that fungal phytopathogens recovered from bentonite-amended soils had more negative correlations (75.6%) with naturally occurring beneficial bacteria and/or fungi than those in non-bentonite soils (65.2%), perhaps suggests, although speculation, that the addition of bentonite promoted soil fungistasis. In summary, our study showed that the addition of bentonite increased maize productivity and reshaped the microbial functional guilds in sandy soils, a consequence of improved soil structure as well as water and nutrient retention; however, the amendment’s long-term impact on soil suppressiveness to fungal phytopathogens is worth further investigation.

Efficacy of Fecal Sampling as a Gut Proxy in the Study of Chicken Gut Microbiota.

Despite the convenience and non-invasiveness of fecal sampling, the fecal microbiota does not fully represent that of the gastrointestinal (GI) tract, and the efficacy of fecal sampling to accurately represent the gut microbiota in birds is poorly understood. In this study, we aim to identify the efficacy of feces as a gut proxy in birds using chickens as a model. We collected 1,026 samples from 206 chickens, including duodenum, jejunum, ileum, cecum, and feces samples, for 16S rRNA amplicon sequencing analyses. In this study, the efficacy of feces as a gut proxy was partitioned to microbial community membership and community structure. Most taxa in the small intestine (84.11–87.28%) and ceca (99.39%) could be identified in feces. Microbial community membership was reflected with a gut anatomic feature, but community structure was not. Excluding shared microbes, the small intestine and ceca contributed 34.12 and 5.83% of the total fecal members, respectively. The composition of Firmicutes members in the small intestine and that of Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria members in the ceca could be well mirrored by the observations in fecal samples (ρ = 0.54–0.71 and 0.71–0.78, respectively, P < 0.001). However, there were few significant correlations for each genus between feces and each of the four gut segments, and these correlations were not high (ρ = −0.2–0.4, P < 0.05) for most genera. Our results suggest that fecal microbial community has a good potential to identify most taxa in the chicken gut and could moderately mirror the microbial structure in the intestine at the microbial population level with phylum specificity. However, it should be interpreted with caution by using feces as a proxy to study associations for microbial structure at individual microorganism level.

Effects of road salt on microbial communities: Halophiles as biomarkers of road salt pollution.

Increased use of salting to de-ice roadways, especially in urban areas, is leading to elevated salinity levels in soil as well as surface- and ground water. This salt pollution may cause long-term ecological changes to soil and aquatic microbial communities. In this study, we examined the impact on microbial communities in soils exposed to urban road salt runoff using both culturing and 16S amplicon sequencing. Both methods showed an increase in halophilic Bacteria and Archaea in samples from road salt-exposed areas and suggested that halophiles are becoming persistent members of microbial communities in urban, road salt-impacted soils. Since salt is a pollutant that can accumulate in soils over time, it is critical to begin assessing its impact on the environment immediately. Toward this goal, we have developed a facile semi-quantitative assay utilizing halophilic microbes as biomarkers to evaluate on-going salt pollution of soils.

Buried Soils as a New Source for Isolation of Biotechnologically Significant Bacterial Strains

Investigation of molecular genetic diversity in paleosoil microbial communities revealed that ~50% of ancient ribotypes were not detected among the ribotypes of the modern microbial communities. Thus, reactivation of ancient microorganisms and investigation of their physiological properties as potentially valuable producers for biotechnology is advisable. The proteolytic bacterial component of paleosoils below burial mounds collected from the vials with votive food at the Peschanyi-4 and Netkachevo burial mounds (15–centuries BC) (Volgograd and Rostov oblasts, Russia) was investigated. Viable cell numbers of heterotrophic bacteria in reactivated samples were (1.5–16.0) × 107 CFU/g soil (growth on LB agar). Using alternating inoculation into liquid media and plating on solid media resulted in isolation of pure cultures of several strains, which were then identified based on analysis of their 16S rRNA gene sequences. Strains of the following species were isolated: Bacillus coagulans (Lactobacillus coagulans), a potentially valuable probiotic; Aquamicrobium terrae, a proteolytic producing surfactants and degrading organic matter; Bacillus cereus, the strain toxicogenic for outbred white mice at intra-abdominal application; Staphylococcus hominis and St. epidermidis, opportunistic pathogens belonging to normal human skin microflora. Apart from Bacillus cereus, all strains exhibited high production of neuroactive amines (DOPA, DOPAC, DA, 5-HTP, HVA, and 3-MT) and amino acids (Asp, Glu, Gly, Tau, and GABA). The strains isolated from the vials with votive food were mostly those associated with humans, rather than typical members of soil microbial communities.

Microbial Succession of Anaerobic Chitin Degradation in Freshwater Sediments.

Chitin is massively produced by freshwater plankton species as a structural element of their exoskeleton or cell wall. At the same time, chitin does not accumulate in the predominantly anoxic sediments, underlining its importance as carbon and nitrogen sources for sedimentary microorganisms. We studied chitin degradation in littoral sediment of Lake Constance, Central Europe's third largest lake. Turnover of the chitin analog methyl-umbelliferyl-N,N-diacetylchitobioside (MUF-DC) was highest in the upper oxic sediment layer, with 5.4 nmol MUF-DC h-1 (g sediment [dry weight])-1 In the underlying anoxic sediment layers, chitin hydrolysis decreased with depth from 1.1 to 0.08 nmol MUF-DC h-1 (g sediment [dry weight])-1 Bacteria involved in chitin degradation were identified by 16S rRNA (gene) amplicon sequencing of anoxic microcosms incubated in the presence of chitin compared to microcosms amended either with N-acetylglucosamine as the monomer of chitin or no substrate. Chitin degradation was driven by a succession of bacteria responding specifically to chitin only. The early phase (0 to 9 days) was dominated by Chitinivibrio spp. (Fibrobacteres). The intermediate phase (9 to 21 days) was characterized by a higher diversity of chitin responders, including, besides Chitinivibrio spp., also members of the phyla Bacteroidetes, Proteobacteria, Spirochaetes, and Chloroflexi In the late phase (21 to 43 days), the Chitinivibrio populations broke down with a parallel strong increase of Ruminiclostridium spp. (formerly Clostridium cluster III, Firmicutes), which became the dominating chitin responders. Our study provides quantitative insights into anaerobic chitin degradation in lake sediments and linked this to a model of microbial succession associated with this activity.IMPORTANCE Chitin is the most abundant biopolymer in aquatic environments, with a direct impact on the carbon and nitrogen cycles. Despite its massive production as a structural element of crustaceans, insects, or algae, it does not accumulate in sediments. Little is known about its turnover in predominantly anoxic freshwater sediments and the responsible microorganisms. We proved that chitin is readily degraded under anoxic conditions and linked this to a succession of the members of the responsible microbial community over a 43-day period. While Fibrobacteres and Firmicutes members were driving the early and late phases of chitin degradation, respectively, a more diverse community was involved in chitin degradation in the intermediate phase. Entirely different microorganisms responded toward the chitin monomer N-acetylglucosamine, which underscores that soluble monomers are poor and misleading substrates to study polymer-utilizing microorganisms. Our study provides quantitative insights into the microbial ecology driving anaerobic chitin degradation in freshwater sediments.

Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters.

Life in water-filled bedrock fissures in the continental deep biosphere is broadly constrained by energy and nutrient availability. Although these communities are alive, robust studies comparing active populations and metabolic processes across deep aquifers are lacking. This study analyzed three oligotrophic Fennoscandian Shield groundwaters, two "modern marine" waters that are replenished with organic carbon from the Baltic Sea and are likely less than 20 years old (171.3 and 415.4 m below sea level) and an extremely oligotrophic "thoroughly mixed" water (448.8 m below sea level) of unknown age that is composed of very old saline and marine waters. Cells were captured either using a sampling device that rapidly fixed RNA under in situ conditions or by filtering flowing groundwater over an extended period before fixation. Comparison of metatranscriptomes between the methods showed statistically similar transcript profiles for the respective water types, and they were analyzed as biological replicates. Study of the small subunit (SSU) rRNA confirmed active populations from all three domains of life, with many potentially novel unclassified populations present. Statistically supported differences between communities included heterotrophic sulfate-reducing bacteria in the modern marine water at 171.3 m below sea level that has a higher organic carbon content than do largely autotrophic populations in the H2- and CO2-fed thoroughly mixed water. While this modern marine water had signatures of methanogenesis, syntrophic populations were predominantly in the thoroughly mixed water. The study provides a first statistical evaluation of differences in the active microbial communities in groundwaters differentially fed by organic carbon or "geogases."IMPORTANCE Despite being separated from the photosynthesis-driven surface by both distance and time, the deep biosphere is an important driver for the earth's carbon and energy cycles. However, due to the difficulties in gaining access and low cell numbers, robust statistical omics studies have not been carried out, and this limits the conclusions that can be drawn. This study benchmarks the use of two separate sampling systems and demonstrates that they provide statistically similar RNA transcript profiles, importantly validating several previously published studies. The generated data are analyzed to identify statistically valid differences in active microbial community members and metabolic processes. The results highlight contrasting taxa and growth strategies in the modern marine waters that are influenced by recent infiltration of Baltic Sea water versus the hydrogen- and carbon dioxide-fed, extremely oligotrophic, thoroughly mixed water.

Performance and Mechanisms of Advanced Nitrogen Removal via FeS-driven Autotrophic Denitrification Coupled with ANAMMOX

Synergy among members of complex microbial communities in the transformation of elements is a key ecological regulation strategy in nature. Making full use of this phenomenon and achieving functional combinations of different microorganisms may have a significant effect on developing new wastewater treatment processes. In this study, nitrogen-containing pollutants were applied in a static batch experiment. The dosage of FeS, the ratio of NO3--N/NO2--N, and the ratio of ANAMMOX (AN) to autotrophic denitrification (AD) biomass were the controlled reaction conditions. The cooperation mechanism resulting from the metabolic complementation of AN and AD is discussed, and the concept of a (AN+AD)TN 0 nitrogen removal process is proposed. This study showed that the excessive dosage of FeS could ensure the more thorough reaction of AD without significantly affecting the metabolic activity of AN bacteria. A complex microbial community was involved in the competition for metabolic substrates when the proportion of NO2--N in the electron acceptor was increased, resulting in a negative impact on the removal of TN. The increase of AN biomass contributed to the strengthening of the cooperation between AN and AD. When the stoichiometric ratio of NH4+-N to NO3--N was less than 0.85, TN could be completely removed. The results showed that a more effective wastewater treatment process may be established by understanding the interactions between microorganisms, and by manipulating or regulating complex microbial communities. This could achieve the efficient removal of pollutants under low material consumption conditions.

Microbial Communities in a Flow-Through Fish Farm for Lumpfish (Cyclopterus lumpus L.) During Healthy Rearing Conditions.

Lumpfish can efficiently remove sea lice from Atlantic salmon in net-pens, and production of lumpfish in closed fish farms is a new, fast developing industry in Norway. However, periodic outbreaks of bacterial diseases in the fish farms represent a large problem, both economically and ethically. Therefore it is important to obtain a better understanding of how microbial communities develop in these production facilities. Knowledge on the characteristics of microbial communities associated with healthy fish could also enable detection of changes associated with disease outbreaks at an early stage. In this study we have monitored microbial communities in a fish farm for lumpfish during normal operational conditions with no disease outbreak by using 16S rRNA gene amplicon sequencing. The study involved weekly samplings of water and biofilms from fish tanks, and fish. The results revealed that the microbial communities in fish tank water were different from the intake water. The water and biofilm in fish tanks were highly similar in regards to microbial community members, but with large differences in relative abundances for some taxa. The sampled fish were associated with mostly the same taxa as in tank water and biofilm, but more variation in relative abundances of different taxonomic groups occurred. The microbial communities in the fish farm seemed stable over time, and were dominated by marine bacteria and archaea within Alphaproteobacteria, Epsilonproteobacteria, Flavobacteria, Gammaproteobacteria, Thaumarchaeota, Planctomycetes, Sphingobacteriia, and Verrucomicrobiae (>10% relative abundance). Bacterial genera known to include fish-pathogenic strains were detected in all types of sample materials, but with low relative abundances (<5%). Exceptions were some samples of fish, biofilm and water with high relative abundance of Tenacibaculum (<85.8%) and Moritella (<82%). In addition, some of the eggs had a high relative abundance of Tenacibaculum (<89.5%). Overall, this study shows that a stable microbial community dominated by various genera of non-pathogenic bacteria is associated with a healthy environment for rearing lumpfish. Taxa with pathogenic members were also part of the microbial communities during healthy conditions, but the stable non-pathogenic bacteria may limit their growth and thereby prevent disease outbreaks.

The Evolution, Ecology, and Mechanisms of Infection by Gram-Positive, Plant-Associated Bacteria.

Gram-positive bacteria are prominent members of plant-associated microbial communities. Although many are hypothesized to be beneficial, some are causative agents of economically important diseases of crop plants. Because the features of Gram-positive bacteria are fundamentally different relative to those of Gram-negative bacteria, the evolution and ecology as well as the mechanisms used to colonize and infect plants also differ. Here, we discuss recent advances in our understanding of Gram-positive, plant-associated bacteria and provide a framework for future research directions on these important plant symbionts.

A GntR-Like Transcription Factor HypR Regulates Expression of Genes Associated With L-Hydroxyproline Utilization in Streptomyces coelicolor A3(2).

Bacteria from the genus Streptomyces have been long exploited as the most prolific producers of antibiotics, other secondary metabolites and enzymes. They are important members of soil microbial communities that can adapt to changing conditions thank to the fine regulation of gene expression in response to environmental signals. Streptomyces coelicolor A3(2) is a model organism for molecular studies with the most deeply recognized interactions within the complex metabolic and regulatory network. However, details about molecular signals recognized by specialized regulatory proteins as well as their direct targets are often missing. We describe here a zinc-binding protein HypR (SCO6294) which belongs to FadR subfamily of GntR-like regulators. The DNA sequence 5′-TACAATGTCAC-3′ recognized by the HypR protein in its own promoter region was identified by DNase I footprinting. Binding of six DNA fragments containing similar sequences located in other promoter regions were confirmed by the electrophoretic mobility shift assay (EMSA). The sequences of 7 in vitro-determined binding sites were assembled to generate a logo of the HypR binding motif, 5′-CTNTGC(A/C)ATGTCAC-3′. Comparison of luciferase reporter genes expression under the control of cloned promoter regions in S. coelicolor A3(2) wild type and deletion mutant strains revealed, that the HypR protein acts as a repressor of its target genes. Genes belonging to the regulon of HypR code for enzymes putatively involved in collagen degradation and utilization of L-hydroxyproline (L-Hyp) as concluded from predicted structure and conserved domains. Their transcription is induced in the wild type strain by the addition of L-Hyp to the culture medium. Moreover, knockout of one of the genes from the predicted L-Hyp utilization operon abolished the ability of the strain to grow on L-Hyp as a sole source of carbon. To our knowledge, this work is the first indication of the existence of the pathway of L-hydroxyproline catabolism in Streptomycetes.

In situ transformation of ethoxylate and glycol surfactants by shale-colonizing microorganisms during hydraulic fracturing.

In the last decade, extensive application of hydraulic fracturing technologies to unconventional low-permeability hydrocarbon-rich formations has significantly increased natural-gas production in the United States and abroad. The injection of surface-sourced fluids to generate fractures in the deep subsurface introduces microbial cells and substrates to low-permeability rock. A subset of injected organic additives has been investigated for their ability to support biological growth in shale microbial community members; however, to date, little is known on how complex xenobiotic organic compounds undergo biotransformations in this deep rock ecosystem. Here, high-resolution chemical, metagenomic, and proteomic analyses reveal that widely-used surfactants are degraded by the shale-associated taxa Halanaerobium, both in situ and under laboratory conditions. These halotolerant bacteria exhibit surfactant substrate specificities, preferring polymeric propoxylated glycols (PPGs) and longer alkyl polyethoxylates (AEOs) over polyethylene glycols (PEGs) and shorter AEOs. Enzymatic transformation occurs through repeated terminal-end polyglycol chain shortening during co-metabolic growth through the methylglyoxal bypass. This work provides the first evidence that shale microorganisms can transform xenobiotic surfactants in fracture fluid formulations, potentially affecting the efficiency of hydrocarbon recovery, and demonstrating an important association between injected substrates and microbial growth in an engineered subsurface ecosystem.

Elucidating the ecological networks in stone-dwelling microbiomes.

Stone surfaces are extreme environments that support microbial life. This microbial growth occurs despite unfavourable conditions associated with stone including limited sources of nutrients and water, high pH and exposure to extreme variations in temperature, humidity and irradiation. These stone-dwelling microbes are often resistant to extreme environments including exposure to desiccation, heavy metals, UV and Gamma irradiation. Here, we report on the effects of climate and stone geochemistry on microbiomes of Roman stone ruins in North Africa. Stone microbiomes were dominated by Actinobacteria, Cyanobacteria and Proteobacteria but were heavily impacted by climate variables that influenced water availability. Stone geochemistry also influenced community diversity, particularly through biologically available P, Mn and Zn. Functions associated with photosynthesis and UV protection were enriched in the metagenomes, indicating the significance of these functions for community survival on stones. Core members of the stone microbial communities were also identified and included Geodermatophilaceae, Rubrobacter, Sphingomonas and others. Our research has helped to expand the understanding of stone microbial community structure and functional capacity within the context of varying climates, geochemical properties and stone conditions.

Key players in the methanogenic biodegradation of n-hexadecane identified by DNA-Stable isotope probing

Methanogenic biodegradation of n-alkanes is an important process in the biogeochemical carbon cycles. The key players in this biochemical processes were investigated for a 920-day of culturing with universally labelled (UL)-13C-hexadecane and 1, 2-13C-hexadecane as the sources of carbon and energy, using stable isotope probing combined with 16S rRNA gene amplification. Results show that the relative abundance of Anaerolineaceae and Tepidiphilus phylotypes increased significantly in the heavy fractions of DNA obtained from the cultures amended with UL-13C-hexadecane and 1, 2-13C-hexadecane, indicating their actively involvement in the transformation and biodegradation of the alkanes by the microbial community. This study provides insights into the active members of the microbial community members in hydrocarbon degradation and is of significant scientific value in further research and relative technology to methanogenic degradation of n-alkanes.

The Infant Gut Microbiota at 12 Months and Its Associations with Maternal Pre-pregnancy BMI, Human Milk Exposure and Infant BMI-for-age Z-score (OR01-05-19)

ObjectivesDetermine if the infant gut microbiota at 12 months of age is associated with maternal pre-pregnancy BMI or infant human milk (HM) exposure. Additionally, determine whether infant BMI z-score at 12 months is associated with the infant microbiota composition and richness at 6 and 12 months. MethodsFecal samples were collected from infants at 6 (n = 35) and 12 (n = 32) months of age. Maternal pre-pregnancy BMI, infant weight and height, and the amount of HM in the infant diet were self-reported. Infant BMI for age z-scores (BAZ) were calculated using WHO Anthro software. Fecal communities were analyzed by 16S rRNA (V4) sequencing on an Illumina Miseq. ResultsInfants who had HM at 12 months had lower microbiota richness than infants who only received it until 6 months or were not exposed. Microbial community membership (Sorensen) was also significantly different in infants who received any HM at 12 months compared to infants who only received it until 6 months or were not exposed. The 12-month microbiota was similar for infants who received HM until 6 months or had no exposure. Infant BAZ at 12 months positively correlated with maternal pre-pregnancy BMI. Fewer infants born to obese women were exposed to HM at 12 months compared to those born to normal weight women. However, HM exposure at 12 months was not associated with infant BAZ at 12 months. In the 12-month microbiota, Shannon diversity also positively correlated with maternal pre-pregnancy BMI. No alpha or beta diversity metrics of the infant microbiota at 6 months were associated with infant BAZ at 12 months. However, the Shannon diversity of the 12-month microbiota tended to be positively associated the 12-month infant BAZ. ConclusionsMaternal pre-pregnancy BMI was associated with higher gut microbiota diversity at 12 months of age. This increase in diversity may influence host metabolism, providing a mechanistic link for elevated BAZ in infants whose mothers had an elevated BMI prior to becoming pregnant. Funding SourcesMichigan State AgBioResearch, Child Health Advances through Research with Mothers, Michigan Health Endowment Fund, and the NIH Environmental Influences on Child Health Outcomes (ECHO) Program (Prenatal Exposures and Child Health Outcomes: A Statewide Study (UG3 OD023285)).

Soil Viruses: A New Hope.

As abundant members of microbial communities, viruses impact microbial mortality, carbon and nutrient cycling, and food web dynamics. Although most of our information about viral communities comes from marine systems, evidence is mounting to suggest that viruses are similarly important in soil. Here I outline soil viral metagenomic approaches and the current state of soil viral ecology as a field, and then I highlight existing knowledge gaps that we can begin to fill. We are poised to elucidate soil viral contributions to terrestrial ecosystem processes, considering: the full suite of potential hosts across trophic scales, the ecological impacts of different viral replication strategies, links to economically relevant outcomes like crop productivity, and measurable in situ virus-host population dynamics across spatiotemporal scales and environmental conditions. Soon, we will learn how soil viruses contribute to food webs linked to organic matter decomposition, carbon and nutrient cycling, greenhouse gas emissions, and agricultural productivity.

Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities.

Metaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the "expressed" metabolism and physiology of microbial community members. However, recently developed metaproteomic tools allow quantification of per-species biomass to determine community structure, in situ carbon sources of community members, and the uptake of labeled substrates by community members. In this perspective, I provide a brief overview of the questions that we can currently address, as well as new metaproteomics-based approaches that we and others are developing to address even more questions in the study of microbial communities and plant and animal microbiota. I also highlight some areas and technologies where I anticipate developments and potentially major breakthroughs in the next 5 years and beyond.

The Water Microbiome Through a Pilot Scale Advanced Treatment Facility for Direct Potable Reuse

Advanced treatment facilities for potable water reuse of wastewater are designed to achieve high removal levels of specific pathogens, as well as many other constituents. However, changes to the microbial community throughout treatment, storage, and distribution of this water have not been well characterized. We applied high-throughput amplicon sequencing, read-based, assembly-based, and genome-resolved metagenomics, and flow cytometry to investigate the microbial communities present in a pilot-scale advanced water treatment facility. Advanced treatment of secondary-treated wastewater consisted of ozonation, chloramination, microfiltration, reverse osmosis (RO), advanced oxidation (UV/H2O2), granular activated carbon (GAC) filtration, and chlorination. Treated water was fed into bench-scale simulated distribution systems (SDS). Cell counts and microbial diversity in bulk water decreased until GAC filtration, and the bacterial communities were significantly different following each treatment step. Bacteria grew within GAC media and contributed to a consistent microbial community in the filtrate, which included members of the Rhizobiales and Mycobacteriaceae. After chlorination, some of the GAC filtrate community was maintained within the SDS, and community shifts were associated with stagnation. Putative antibiotic resistance genes and potential opportunistic pathogens were identified before RO and after advanced oxidation, although few if any members of the wastewater microbial community passed through these treatment steps. These findings can contribute to improved design of advanced treatment trains and management of microbial communities in post-treatment steps.

Different response of bacteria, archaea and fungi to process parameters in nine full-scale anaerobic digesters.

SummaryBiogas production is a biotechnological process realized by complex bacterial, archaeal and likely fungal communities. Their composition was assessed in nine full‐scale biogas plants with distinctly differing feedstock input and process parameters. This study investigated the actually active microbial community members by using a comprehensive sequencing approach based on ribosomal 16S and 28S rRNA fragments. The prevailing taxonomical units of each respective community were subsequently linked to process parameters. Ribosomal rRNA of bacteria, archaea and fungi, respectively, showed different compositions with respect to process parameters and supplied feedstocks: (i) bacterial communities were affected by the key factors temperature and ammonium concentration; (ii) composition of archaea was mainly related to process temperature; and (iii) relative abundance of fungi was linked to feedstocks supplied to the digesters. Anaerobic digesters with a high methane yield showed remarkably similar bacterial communities regarding identified taxonomic families. Although archaeal communities differed strongly on genus level from each other, the respective digesters still showed high methane yields. Functional redundancy of the archaeal communities may explain this effect. 28S rRNA sequences of fungi in all nine full‐scale anaerobic digesters were primarily classified as facultative anaerobic Ascomycota and Basidiomycota. Since the presence of ribosomal 28S rRNA indicates that fungi may be active in the biogas digesters, further research should be carried out to examine to which extent they are important players in anaerobic digestion processes.

Islands in the stream: from individual to communal fiber degradation in the rumen ecosystem.

ABSTRACTThe herbivore rumen ecosystem constitutes an extremely efficient degradation machinery for the intricate chemical structure of fiber biomass, thus, enabling the hosting animal to digest its feed. The challenging task of deconstructing and metabolizing fiber is performed by microorganisms inhabiting the rumen. Since most of the ingested feed is comprised of plant fiber, these fiber-degrading microorganisms are of cardinal importance to the ecology of the rumen microbial community and to the hosting animal, and have a great impact on our environment and food sustainability. We summarize herein the enzymological fundamentals of fiber degradation, how the genes encoding these enzymes are spread across fiber-degrading microbes, and these microbes' interactions with other members of the rumen microbial community and potential effect on community structure. An understanding of these concepts has applied value for agriculture and our environment, and will also contribute to a better understanding of microbial ecology and evolution in anaerobic ecosystems.