Bacterial Community Metabolism Research Articles

Characteristics of humification, functional enzymes and bacterial community metabolism during manganese dioxide-added composting of municipal sludge

The aim of this study was to assess effects of MnO2 addition (CK-0%, T1-2% and T2-5%) on humification and bacterial community during municipal sludge (MS) composting. The results suggested that MnO2 addition inhibited the growth of Nitrospira but stimulated Nonomuraea, Actinomadura, Streptomyces and Thermopolyspora, facilitating the lignocellulose degradation and humification with the increase in organic matter degradation by 13.8%–19.2% and humic acid content by 10.9%–20.6%. Compared to CK, the abundances of exoglucanase (EC:3.2.1.91), endo-1,4-beta-xylanase (EC:3.2.1.136) and endomannanase (EC:3.2.1.78) increased by 88–99, 52–66 and 4–15 folds, respectively. However, 5%-MnO2 induced the enrichment of Mizugakiibacter that harms the environment of agricultural production. The addition of 2%-MnO2 was recommended for MS composting. Furthermore, metabolic function analysis indicated that MnO2 addition altered amino acid and carbohydrate metabolism, especially enhancing propanoate metabolism and butanoate metabolism but inhibiting citrate cycle. Structural equation modeling revealed that Nonomuraea and Actinomadura were the main drivers for lignocellulose degradation. This study provided theoretical guidance in regulating humification via MnO2 for MS composting.

Effects of Long-term Tillage on Soil Bacterial Community Structure and Physicochemical Properties of Dryland Wheat Fields in Northern China

To explore the effects of long-term tillage on bacterial community structure in different soil layers of dryland wheat fields and its relationship with soil physicochemical properties, a long-term field experiment was conducted from 2016 to 2021 in Wenxi Experimental Demonstration Base of Shanxi Agricultural University, Shanxi Province. We studied the effects of no-tillage (NT), subsoiling-tillage (ST), and deep plowing (DP) on soil physicochemical properties; α and β diversity of the bacterial community; and dominant and different species of phyla and genera in different soil layers. Additionally, PICRUSt2 was used to predict the metabolic function of soil bacterial community. The results revealed that subsoiling-tillage and deep plowing significantly increased the soil water content in the 20-40 cm soil layer and significantly decreased the soil organic carbon content in the 0-20 cm soil layer compared with that under no-tillage for five consecutive years. Compared with that under deep plowing, subsoiling-tillage significantly increased soil water content, soil organic carbon content, dissolved organic carbon content, and dissolved organic nitrogen content in the 0-20 cm soil layer. Compared with that under no-tillage, subsoiling-tillage and deep plowing increased the α diversity of the soil bacterial community in the 0-40 cm soil layer, and subsoiling-tillage was higher than deep plowing. Compared with that under no-tillage, subsoiling-tillage and deep plowing significantly increased the relative abundances of Acidobacteria and Nitrospirae in the 0-20 cm soil layer and Acidobacteria, Chloroflexi, Gemmatimonadetes, Rokubacteria, GAL15, and Nitrospirae in the 20-40 cm soil layer. Compared with that under no-tillage, subsoiling-tillage and deep plowing significantly increased the relative abundance of Nitrospira in the 0-20 cm soil layer and Rubrobacter and Streptomyces in the 20-40 cm soil layer. Compared with that under deep plowing, subsoiling-tillage significantly increased the relative abundance of Acidobacteria and Gemmatimonadetes in the 0-40 cm soil layer. Redundancy analysis demonstrated that the contents of soil organic carbon, dissolved organic carbon, and dissolved organic nitrogen in the 0-20 cm soil layer exerted positive effects on Actinobacteria and Blastococcus, and the soil water content in the 0-40 cm soil layer exerted positive effects on Acidobacteria, Chloroflexi, and Gemmatimonadetes under subsoiling-tillage. The results of PICRUSt2 prediction showed that subsoiling-tillage and deep plowing significantly increased the relative abundance of amino acid metabolism and the metabolism of cofactors and vitamins but decreased the relative abundance of lipid metabolism of bacterial communities in the 20-40 cm soil layer compared with that under no-tillage. Compared with that under deep plowing, subsoiling-tillage significantly increased the relative abundances of amino acid metabolism in the 0-40 cm soil layer and other amino acid metabolism in the 0-20 cm soil layer. In conclusion, subsoiling-tillage or deep plowing could increase the soil water content, α diversity of the soil bacterial community, and their metabolic capacity in the dryland wheat fields during the summer fallow period. The relative abundance of Acidobacteria and Gemmatimonadetes and the ability of amino acid metabolism of the bacterial community were increased by subsoiling-tillage, and thus the contents of soil dissolved organic carbon and dissolved nitrogen can be increased.

Effects of phosphate-solubilizing bacteria on phosphorus components, humus and bacterial community metabolism during spent mushroom substrate composting

To address the low conversion of effective phosphorus during previous studies on spent mushroom substrate (SMS) composting, phosphorus-solubilizing bacteria (PSB) were utilized to increase the effective phosphorus content in this study. The results demonstrated that PSB treatments exhibited higher temperature levels up to 66 °C. The TN, NH4+-N, and NO3−-N contents were higher than those of the control treatment (CK) by 9.01%, 50.01%, and 4.61%, respectively. Inoculation with PSB increased effective phosphorus, total phosphorus, and humus content in the SMS compost by 6.84%, 11.05%, and 9.10%. In addition, based on PICRUSt analysis, inoculation with PSB significantly promoted metabolic pathways associated with phosphorus conversion or the production of substances that can facilitate phosphorus conversion or phosphorus leaching, thus improving phosphorus utilization in compost. In conclusion, the addition of PSB can improve the bioavailability of P and the humus content in SMS compost to realize the green and sustainable development of the edible mushroom industry.

The influences of acidic electrolyzed water on quality and bacteria community of fresh-cut jackfruit in storage

Abstract This study evaluated the effects of acidic electrolyzed oxidizing water (AEW) on the quality and bacterial communities of fresh-cut jackfruit during storage. The result showed that AEW treatment, as compared to the CK group (without AEW treatment), could effectively inhibit the browning, maintain higher firmness and higher amounts of total titratable acidity (TTA) (0.21%), sugars (58.30 g/kg), ascorbic acids (28.72 mg/kg) and total phenolics (35.47 mg/kg) of fresh-cut jackfruits, and suppress the decrease of antioxidant ability during 4–8 days of storage. Additionally, the bacterial communities were significantly affected by AEW during storage. In particular, the AEW treated samples showed lower abundance of Pseudomonas and Lactobacillus than the CK group after storage of 8 day. And energy metabolism, nucleotide metabolism has the significantly lower (p < 0.05) relative abundance in the AEW group than in CK group. These results suggested that AEW (pH: 4.2–4.5, ACC: 35–38 mg/L) treatment could maintain the quality of fresh-cut jackfruit during storage. It could be attributed to that AEW treatment affect the growth and metabolism of bacterial communities, resulting in the decrease of nutrients consumption.

Harnessing Paenarthrobacter ureafaciens YL1 and Pseudomonas koreensis YL2 Interactions to Improve Degradation of Sulfamethoxazole.

Sulfamethoxazole (SMX) is a widespread and persistent pollutant in the environment. Although the screening and analysis of SMX-degrading bacteria have been documented, the interaction mechanisms of functional microorganisms are still poorly understood. This study constructed a consortium with strain YL1 and YL2 supplied with SMX as the sole carbon and energy source. The coexisting mechanism and the removal of SMX of the consortium were investigated. The total oxidizable carbon (TOC) removal rate of the combined bacterial system was 38.94% compared to 29.45% for the single bacterial system at the same biomass. The mixed bacterial consortium was able to resist SMX at concentrations up to 400 mg/L and maintained a stable microbial structure at different culture conditions. The optimum conditions found for SMX degradation were 30 °C, pH 7.0, a shaking speed of 160 r·min−1, and an initial SMX concentration of 200 mg·L−1. The degradation of SMX was accelerated by the addition of YL2 for its ability to metabolize the key intermediate, 4-aminophenol. The removal rate of 4-aminophenol by strain YL2 reached 19.54% after 5 days. Genome analysis revealed that adding riboflavin and enhancing the reducing capacity might contribute to the degradation of SMX. These results indicated that it is important for the bioremediation of antibiotic-contaminated aquatic systems to understand the metabolism of bacterial communities.

New insights into metabolomics profile generation in fermented tea: the relevance of bacteria and metabolites in Fuzhuan brick tea.

The contribution of bacteria to fermented tea is not clear and the associated research is relatively limited. To reveal the role of microorganisms in fermented tea processing, the microbial community and metabolites of Fuzhuan brick tea (FBT), a Chinese traditional fermented tea, were revealed via high-throughput sequencing and liquid chromatography-mass spectrometry (LC-MS). In FBT, bacterial communities had a higher abundance and diversity, Lactococcus and Bacillus were the main bacteria, and Eurotium was the predominant fungus. The predictive metabolic function indicated the pathways of cellular growth, environmental information, genetics and material metabolism of bacterial communities were abundant, whereas the fungal community predictive metabolic function was almost saprotroph. Using LC-MS, 1143 and 536 metabolites were defined in positive and negative ion mode, respectively. There were essential correlations between bacterial populations and metabolites, such that Bacillus was correlated significantly with 44 metabolites (P < 0.05) and Enterococcus was significantly associated with 15 metabolites (P < 0.05). Some of the main active components were significantly correlated with the bacteria, such as Enterococcus, Lactococcus and Carnobacterium. Not only Eurotium, but also the bacteria were involved in the changes of metabolomics profile in fermented FBT. The present study assists in providing new insights into metabolomics profile generation in fermented tea. The present research lays a foundation for controlling the FBT fermentation by artificial inoculation to improve quality. © 2021 Society of Chemical Industry.

Graphene-Based Nanomaterials Modulate Internal Biofilm Interactions and Microbial Diversity

Graphene-based nanomaterials (GBMs), such as graphene oxide (GO) and reduced graphene oxide (rGO), possess unique properties triggering high expectations for the development of new technological applications and are forecasted to be produced at industrial-scale. This raises the question of potential adverse outcomes on living organisms and especially toward microorganisms constituting the basis of the trophic chain in ecosystems. However, investigations on GBMs toxicity were performed on various microorganisms using single species that are helpful to determine toxicity mechanisms but fail to predict the consequences of the observed effects at a larger organization scale. Thus, this study focuses on the ecotoxicological assessment of GO and rGO toward a biofilm composed of the diatom Nitzschia palea associated to a bacterial consortium. After 48 and 144 h of exposure to these GBMs at 0, 0.1, 1, and 10 mg.L−1, their effects on the diatom physiology, the structure, and the metabolism of bacterial communities were measured through the use of flow cytometry, 16S amplicon sequencing, and Biolog ecoplates, respectively. The exposure to both of these GBMs stimulated the diatom growth. Besides, GO exerted strong bacterial growth inhibition as from 1 mg.L−1, influenced the taxonomic composition of diatom-associated bacterial consortium, and increased transiently the bacterial activity related to carbon cycling, with weak toxicity toward the diatom. On the contrary, rGO was shown to exert a weaker toxicity toward the bacterial consortium, whereas it influenced more strongly the diatom physiology. When compared to the results from the literature using single species tests, our study suggests that diatoms benefited from diatom-bacteria interactions and that the biofilm was able to maintain or recover its carbon-related metabolic activities when exposed to GBMs.

Different lactic acid bacteria and their combinations regulated the fermentation process of ensiled alfalfa: ensiling characteristics, dynamics of bacterial community and their functional shifts.

SummaryThe objectives of this study were to investigate the adaptation and competition of Lactobacillus plantarum, Pediococcus pentosaceus and Enterococcus faecalis inoculated in alfalfa silage alone or in combination on the fermentation quality, dynamics of bacterial community, and their functional shifts using single‐molecule real‐time (SMRT) sequencing technology. Before ensiling, alfalfa was inoculated with L. plantarum (Lp), P. pentosaceus (Pp), E. faecalis (Ef) or their combinations (LpPp, LpEf, LpPpEf) and sampled at 1, 3, 7, 14 and 60 days. After 60‐days fermentation, the Lp‐, Pp‐ and LpPp‐inoculated silages had lower pH but greater concentrations of lactic acid were observed in Pp, LpEf and LpPpEf‐inoculated silages. The inoculants altered the keystone taxa and the bacterial community dynamics in different manners, where L. plantarum, Weissella cibaria and L. pentosaceus dominated the bacterial communities after 14 days‐fermentation in all treatments. The silages with better fermentation quality had simplified bacterial correlation structures. Moreover, different inoculants dramatically changed the carbohydrate, amino acid, energy, nucleotide and vitamin metabolism of bacterial communities during ensiling. Results of the current study indicate that effect of different inoculants on alfalfa silage fermentation was implemented by modulating the succession of bacterial community, their interactions and metabolic pathways as well during ensiling.

Effects of swine manure composting by microbial inoculation: Heavy metal fractions, humic substances, and bacterial community metabolism

This study aimed to investigate the effect of swine manure composting with microbial inoculation (MI) and without MI (CK) on heavy metal (Cr, Cd, and Pb) fractions, humic substance (HS), and metabolism pathway. The results showed that MI could passivate the heavy metal Cr and reduce the proportion of exchangeable (EXC) fraction of Cd, but it does not affect the EXC fraction of Pb. Compared to CK, HS, humic acid (HA), and fulvic acid (FA) were significantly increased with MI at the maturity stage. The propagation of Proteobacteria (day 4) and Firmicutes (days 12 and 24) was strengthened with MI. Canonical correlation analysis found that HA and Firmicutes were positively correlated with heavy metal (Cr, Cd, and Pb) residual (RES) fraction, and FA was positively correlated with Proteobacteria. Moreover, MI can significantly increase amino acid metabolism and carbohydrate metabolism by day 4, enhance the metabolism of enzyme families and glycan biosynthesis by day 12, and improve membrane transport. Overall, MI could facilitates the increase in HA and FA content and transfer of heavy metal (Cr, Cd, and Pb) fractions, it particularly helps increase the RES fraction.

Computational modeling of the gut microbiota reveals putative metabolic mechanisms of recurrent Clostridioides difficile infection.

Approximately 30% of patients who have Clostridioides difficile infection (CDI) will suffer at least one incident of reinfection. While the underlying causes of CDI recurrence are poorly understood, interactions between C. difficile and commensal gut bacteria are thought to play an important role. In this study, an in silico pipeline was used to process 16S rRNA gene amplicon sequence data of 225 stool samples from 93 CDI patients into sample-specific models of bacterial community metabolism. Clustered metabolite production rates generated from post-diagnosis samples generated a high Enterobacteriaceae abundance cluster containing disproportionately large numbers of recurrent samples and patients. This cluster was predicted to have significantly reduced capabilities for secondary bile acid synthesis but elevated capabilities for aromatic amino acid catabolism. When applied to 16S sequence data of 40 samples from fecal microbiota transplantation (FMT) patients suffering from recurrent CDI and their stool donors, the community modeling method generated a high Enterobacteriaceae abundance cluster with a disproportionate large number of pre-FMT samples. This cluster also was predicted to exhibit reduced secondary bile acid synthesis and elevated aromatic amino acid catabolism. Collectively, these in silico predictions suggest that Enterobacteriaceae may create a gut environment favorable for C. difficile spore germination and/or toxin synthesis.

Coexisting mechanisms of bacterial community are changeable even under similar stable conditions in a chemostat culture

The coexisting mechanism of a synthetic bacterial community (SBC) was investigated to better understand how to manage microbial communities. The SBC was constructed with three kinds of phenol-utilizing bacteria, Pseudomonas sp. LAB-08, Comamonas testosteroni R2, and Cupriavidus sp. P-10, under chemostat conditions supplied with phenol as a sole carbon and energy source. Population densities of all strains were monitored by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase. Although the supply of phenol was stopped to allow perturbation in the SBC, all of the strains coexisted and the degradation of phenol was maintained for more than 800 days. The qPCR analyses showed that strains LAB-08 and R2 became dominant simultaneously, whereas strain P-10 was a minor population. This phenomenon was observed before and after the phenol-supply stoppage. The kinetic parameters for phenol of the SBC changed before and after the phenol-supply stoppage, which suggests a change in functional roles of strains in the SBC. Transcriptional levels of phenol hydroxylase and catechol dioxygenases of three strains were monitored by reverse-transcription qPCR (RT-qPCR). The RT-qPCR analyses revealed that all strains shared phenol and survived independently before the phenol-supply stoppage. After the stoppage, strain P-10 would incur the cost for degradation of phenol and catechol, whereas strains LAB-08 and R2 seemed to be cheaters using metabolites, indicating the development of the metabolic network. These results indicated that it is important for the management and redesign of microbial communities to understand the metabolism of bacterial communities.

Recurrent seasonal changes in bacterial growth efficiency, metabolism and community composition in coastal waters.

The microbial response to environmental changes in coastal waters of the eastern Cantabrian Sea was explored for four years by analysing a broad set of environmental variables along with bacterial community metabolism and composition. A recurrent seasonal cycle emerged, consisting of two stable periods, characterized by low bacterial metabolic activity (winter) from October to March, and high bacterial metabolic activity (summer) from May to August. These two contrasting periods were linked by short transition periods in April (TA ) and September (TS ). The phylogenetic groups Alphaproteobacteria and Bacteroidetes were dominant during winter and summer respectively, and their recurrent alternation was mainly driven by the bloom of eukaryotic phytoplankton before TA and the bloom of prokaryotic phytoplankton before TS . Bacterial growth efficiency remained high and stable during the winter and summer periods but dropped during the two short transition periods. Our results suggest that bacterial growth efficiency should be considered a very resilient property that reflects different stages in the adaptation of the bacterial community composition to the environmental changes occurring throughout the seasonal cycle in this coastal ecosystem.

Decreasing diversity of rare bacterial subcommunities relates to dissolved organic matter along permafrost thawing gradients

Dissolved organic matter (DOM) released from permafrost thaw greatly influences the biogeochemical cycles of, among others, downstream carbon, nitrogen and phosphorus cycles; yet, knowledge of the linkages between bacterial communities with permafrost DOM heterogeneity is limited. Here, we aim at unravelling the responses of bacterial diversities and metabolic profiles to DOM quantity and composition across permafrost thawing gradients by coupling an extensive field investigation with bio-incubation experiments. Richness, evenness and dissimilarities of the whole and rare communities decreased from thermokarst pits to headstreams and to downstream rivers. The assemblages of the abundant subcommunities were mainly determined by ecological drift-driven stochastic processes. Both the optical and the molecular composition of DOM were significantly related to the changes of the whole (rare) bacterial communities (Mantel’s correlation > 0.5, p < 0.01). Diversity indices of the whole and rare communities decreased with decreasing relative abundance of tannins, condensed aromatics and more aromatic and oxidized lignins as well as with decreased dissolved organic carbon and intensities of all fluorescence components. Laboratory DOM bio-incubation experiments further confirmed microbial consumption of more aromatic and oxidized compounds as well as decreasing metabolic diversities in terms of microbial degradation and production along permafrost thawing gradients. Our findings suggest that changes in the sources of permafrost-derived DOM induced by global warming can have different influences on the diversity and metabolism of bacterial communities and thus on permafrost carbon climate feedbacks along permafrost thawing gradients.

The Origin, Succession, and Predicted Metabolism of Bacterial Communities Associated with Leaf Decomposition.

Intraspecific variation in plant nutrient and defensive traits can regulate ecosystem-level processes, such as decomposition and transformation of plant carbon and nutrients. Understanding the regulatory mechanisms of ecosystem functions at local scales may facilitate predictions of the resistance and resilience of these functions to change. We evaluated how riverine bacterial community assembly and predicted gene content corresponded to decomposition rates of green leaf inputs from red alder trees into rivers of Washington State, USA. Previously, we documented accelerated decomposition rates for leaves originating from trees growing adjacent to the site of decomposition versus more distant locales, suggesting that microbes have a "home-field advantage" in decomposing local leaves. Here, we identified repeatable stages of bacterial succession, each defined by dominant taxa with predicted gene content associated with metabolic pathways relevant to the leaf characteristics and course of decomposition. "Home" leaves contained bacterial communities with distinct functional capacities to degrade aromatic compounds. Given known spatial variation of alder aromatics, this finding helps explain locally accelerated decomposition. Bacterial decomposer communities adjust to intraspecific variation in leaves at spatial scales of less than a kilometer, providing a mechanism for rapid response to changes in resources such as range shifts among plant genotypes. Such rapid responses among bacterial communities in turn may maintain high rates of carbon and nutrient cycling through aquatic ecosystems.IMPORTANCE Community ecologists have traditionally treated individuals within a species as uniform, with individual-level biodiversity rarely considered as a regulator of community and ecosystem function. In our study system, we have documented clear evidence of within-species variation causing local ecosystem adaptation to fluxes across ecosystem boundaries. In this striking pattern of a "home-field advantage," leaves from individual trees tend to decompose most rapidly when immediately adjacent to their parent tree. Here, we merge community ecology experiments with microbiome approaches to describe how bacterial communities adjust to within-species variation in leaves over spatial scales of less than a kilometer. The results show that bacterial community compositional changes facilitate rapid ecosystem responses to environmental change, effectively maintaining high rates of carbon and nutrient cycling through ecosystems.

Effects of elevated CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; and phytoplankton-derived organic matter on the metabolism of bacterial communities from coastal waters

Abstract. Microcosm experiments to assess the bacterioplankton's response to phytoplankton-derived organic matter obtained under current and future ocean CO2 levels were performed. Surface seawater enriched with inorganic nutrients was bubbled for 8 days with air (current CO2 scenario) or with a 1000 ppm CO2 air mixture (future CO2 scenario) under solar radiation. The organic matter produced under the current and future CO2 scenarios was subsequently used as an inoculum. Triplicate 12 L flasks filled with 1.2 µm of filtered natural seawater enriched with the organic matter inocula were incubated in the dark for 8 days under CO2 conditions simulating current and future CO2 scenarios, to study the bacterial response. The acidification of the media increased bacterial respiration at the beginning of the experiment, while the addition of the organic matter produced under future levels of CO2 was related to changes in bacterial production and abundance. This resulted in a 67 % increase in the integrated bacterial respiration under future CO2 conditions compared to present CO2 conditions and 41 % higher integrated bacterial abundance with the addition of the acidified organic matter compared to samples with the addition of non acidified organic matter. This study demonstrates that the increase in atmospheric CO2 levels can impact bacterioplankton metabolism directly, by changes in the respiration rate, and indirectly, by changes on the organic matter, which affected bacterial production and abundance.

Gut Dysbiosis With Bacilli Dominance and Accumulation of Fermentation Products Precedes Late-onset Sepsis in Preterm Infants.

Gut dysbiosis has been suggested as a major risk factor for the development of late-onset sepsis (LOS), a main cause of mortality and morbidity in preterm infants. We aimed to assess specific signatures of the gut microbiome, including metabolic profiles, in preterm infants <34 weeks of gestation preceding LOS. In a single-center cohort, fecal samples from preterm infants were prospectively collected during the period of highest vulnerability for LOS (days 7, 14, and 21 of life). Following 16S rRNA gene profiling, we assessed microbial community function using microbial metabolic network modeling. Data were adjusted for gestational age and use of probiotics. We studied stool samples from 71 preterm infants with LOS and 164 unaffected controls (no LOS/necrotizing enterocolitis). In most cases, the bacteria isolated in diagnostic blood culture corresponded to the genera in the gut microbiome. LOS cases had a decelerated development of microbial diversity. Before onset of disease, LOS cases had specific gut microbiome signatures with higher abundance of Bacilli (specifically coagulase-negative Staphylococci) and a lack of anaerobic bacteria. In silico modeling of bacterial community metabolism suggested accumulation of the fermentation products ethanol and formic acid in LOS cases before the onset of disease. Intestinal dysbiosis preceding LOS is characterized by an accumulation of Bacilli and their fermentation products and a paucity of anaerobic bacteria. Early microbiome and metabolic patterns may become a valuable biomarker to guide individualized prevention strategies of LOS in highly vulnerable populations.

Genomic and Transcriptomic Resolution of Organic Matter Utilization Among Deep-Sea Bacteria in Guaymas Basin Hydrothermal Plumes.

Microbial chemosynthesis within deep-sea hydrothermal vent plumes is a regionally important source of organic carbon to the deep ocean. Although chemolithoautotrophs within hydrothermal plumes have attracted much attention, a gap remains in understanding the fate of organic carbon produced via chemosynthesis. In the present study, we conducted shotgun metagenomic and metatranscriptomic sequencing on samples from deep-sea hydrothermal vent plumes and surrounding background seawaters at Guaymas Basin (GB) in the Gulf of California. De novo assembly of metagenomic reads and binning by tetranucleotide signatures using emergent self-organizing maps (ESOM) revealed 66 partial and nearly complete bacterial genomes. These bacterial genomes belong to 10 different phyla: Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria, Verrucomicrobia. Although several major transcriptionally active bacterial groups (Methylococcaceae, Methylomicrobium, SUP05, and SAR324) displayed methanotrophic and chemolithoautotrophic metabolisms, most other bacterial groups contain genes encoding extracellular peptidases and carbohydrate metabolizing enzymes with significantly higher transcripts in the plume than in background, indicating they are involved in degrading organic carbon derived from hydrothermal chemosynthesis. Among the most abundant and active heterotrophic bacteria in deep-sea hydrothermal plumes are Planctomycetes, which accounted for seven genomes with distinct functional and transcriptional activities. The Gemmatimonadetes and Verrucomicrobia also had abundant transcripts involved in organic carbon utilization. These results extend our knowledge of heterotrophic metabolism of bacterial communities in deep-sea hydrothermal plumes.

Molecular Evidence for Metabolically Active Bacteria in the Atmosphere.

Bacterial metabolisms are responsible for critical chemical transformations in nearly all environments, including oceans, freshwater, and soil. Despite the ubiquity of bacteria in the atmosphere, little is known about the metabolic functioning of atmospheric bacterial communities. To gain a better understanding of the metabolism of bacterial communities in the atmosphere, we used a combined empirical and model-based approach to investigate the structure and composition of potentially active bacterial communities in air sampled at a high elevation research station. We found that the composition of the putatively active bacterial community (assayed via rRNA) differed significantly from the total bacterial community (assayed via rDNA). Rare taxa in the total (rDNA) community were disproportionately active relative to abundant taxa, and members of the order Rhodospirillales had the highest potential for activity. We developed theory to explore the effects of random sampling from the rRNA and rDNA communities on observed differences between the communities. We found that random sampling, particularly in cases where active taxa are rare in the rDNA community, will give rise to observed differences in community composition including the occurrence of “phantom taxa”, taxa which are detected in the rRNA community but not the rDNA community. We show that the use of comparative rRNA/rDNA techniques can reveal the structure and composition of the metabolically active portion of bacterial communities. Our observations suggest that metabolically active bacteria exist in the atmosphere and that these communities may be involved in the cycling of organic compounds in the atmosphere.

Resource niche overlap promotes stability of bacterial community metabolism in experimental microcosms.

Decomposition of organic matter is an important ecosystem process governed in part by bacteria. The process of decomposition is expected to benefit from interspecific bacterial interactions such as resource partitioning and facilitation. However, the relative importance of resource niche breadth (metabolic diversity) and resource niche overlap (functional redundancy) on decomposition and the temporal stability of ecosystem processes received little scientific attention. Therefore, this study aims to evaluate the effect of an increase in bacterial community resemblance on both decomposition and the stability of bacterial metabolism in aquatic sediments. To this end, we performed laboratory microcosm experiments in which we examined the influence of bacterial consortia differing in number and composition of species on bacterial activity (Electron Transport System Activity, ETSA), dissolved organic carbon production and wavelet transformed measurements of redox potential (Eh). Single substrate affinities of the individual bacterial species were determined in order to calculate the metabolic diversity of the microbial community. Results presented here indicate that bacterial activity and organic matter decomposition increase with widening of the resource niche breadth, and that metabolic stability increases with increasing overlap in bacterial resource niches, hinting that resource niche overlap can promote the stability of bacterial community metabolism.

Structure and Functional Metabolism of Bacterial Communities on Leaves of Typical Urban Greening Tree Species

Structure and Functional Metabolism of Bacterial Communities on Leaves of Typical Urban Greening Tree Species