Community Functional Potential Research Articles

Temporal and functional interrelationships between bacterioplankton communities and the development of a toxigenic Microcystis bloom in a lowland European reservoir

The cyanobacteria-associated microbiome is constantly reshaped by bloom development. However, the synergistic-antagonistic nature of the relationships between Microcystis and its microbiome still remains unclear. Therefore, temporal changes of bacterioplankton communities and their functional potential through different developing stages of a Microcystis toxigenic bloom were investigated, considering bacterioplankton assemblages as particle-attached (PAB) and free-living (FLB) bacteria. 16S rRNA sequencing revealed that PAB were represented by Proteobacteria and Cyanobacteria, while FLB by Proteobacteria and Actinobacteria. Network and ordination analyses indicated that PAB inter-relationships were more complex—numerous connections between taxa with stronger correlations, than FLB—rather influenced by physico-chemical parameters. PAB in pre-summer was diverse with Proteobacteria containing potential taxa involved in nitrogen-transforming processes. In mid-summer, PAB presented a mix-bloom dominated by Snowella, Aphanizomenon, and Microcystis, which were succeeded by toxigenic Microcystis in post-summer. Both periods were associated to potential taxa with parasitic/predatory lifestyles against cyanobacteria. In post-summer, Sutterellaceae were recognized as poor water quality indicators, and their strong association with Microcystis could have represented an increased threat for that period. Microcystis was a major factor significantly reducing PAB diversity and evenness, suggesting that it negatively influenced bacterioplankton assemblages, probably also altering the overall community functional potential.

Microbial Community and Metabolite Dynamics During Soy Sauce Koji Making.

Koji making is a pre-fermentation stage in soy sauce manufacturing that impacts final product quality. Previous studies have provided valuable insights into the microbial species present in koji. However, changes in microbial community functional potential during koji-making are not well-known, nor are the associations among microbial populations and flavoring characteristics. In the present study, we investigated the succession of microbial communities, microbial community functional potential, metabolite profiles, and associations among microbial community members/functions with metabolites during koji making using shotgun metagenomic and metabolomic analyses. Firmicutes, Proteobacteria, and Ascomycota were identified as the most abundant microbial phyla in early koji making (0–12 h). Aspergillus (fungi) and Weissella (bacteria) exhibited marked abundance increases (0.98–38.45% and 0.31–30.41%, respectively) after 48 h of fermentation. Metabolite analysis revealed that aspartic acid, lysine, methyl acetate, isovaleraldehyde, and isoamyl alcohol concentrations increased ∼7-, 9-, 5-, 49-, and 10-fold after 48 h of fermentation. Metagenomic profiling demonstrated that koji communities were dominated by genes related to carbohydrate metabolism and amino acid metabolism, but functional profiles exhibited marked shifts after 24 h of fermentation. The abundances of genes within the categories of carbohydrate and amino acid metabolism all increased during koji making, except for pyruvate metabolism, glycolysis/gluconeogenesis, and the citrate cycle. Correlational analyses indicated that Aspergillus, Lactococcus, Enterococcus, Corynebacterium, and Kocuria abundances were positively correlated with 15 amino acid concentrations (all p < 0.05), while Weissella abundances were positively correlated with concentrations of volatile flavor compounds, including eight amino acids, phenylacetaldehyde, acetic acid, 2,3-butanediol, ethyl acetate, and ethanol (p < 0.05). These results provide valuable information for understanding the microbial-associated mechanisms of flavor formation during koji making.

Taxonomic and nitrogen-cycling microbial community functional profiles of sugarcane and adjacent forest soils in Southeast Brazil

Nowadays, due to the expansion of agricultural borders, it is highly desirable to increase the sustained productivity of sugarcane cultivars using the knowledge of soil microbial communities. In this study, twelve shotgun metagenomic datasets based on genomic DNA from soil were analyzed using the Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) and Statistical Analysis of Metagenomic Profiles (STAMP) to assess differential responses for the total soil bacterial community composition and nitrogen-cycling microbial community functional potential in soils from sugarcane field with pre-harvest burning and adjacent forest in dry and wet seasons in Southeast Brazil. The soil bacterial community revealed higher abundance for Actinobacteria in forest soil than sugarcane soil in dry and wet seasons, and an opposite pattern for Proteobacteria and Planctomycetes in these soils in both seasons. The results obtained in this study based on the KEEG map suggest that the forest soil has a higher nitrogen-cycling microbial community functional potential compared to the sugarcane soil, independently of the season. The gene sequences associated with carbohydrate metabolism were the most frequent in all soil metagenomes. Taken together, the results confirm previous findings regarding the effects of forest conversion to sugarcane production area, providing new insights regarding to this conversion through the prism of the seasonality and pre-harvesting method on microbially mediated nitrogen cycle in sugarcane production fields.

Microbial Functional Diversity in Vineyard Soils: Sulfur Metabolism and Links With Grapevine Plants and Wine Quality

The quality of the vineyard soils has a direct impact on grapes and wine quality and represents a key component of the “Terroir concept”. However, information on the impact of soil microbiota on grapevine plants and wine quality are generally lacking. In fact, over the last few years most of the attempts made to correlate soil microbial communities and wine quality were limited by overlooking both the functional traits of soil microbiota and the spatial variability of vineyards soils. In this work, we used a functional gene microarray approach (GeoChip) and soil enzymatic analyses to assess the soil microbial community functional potential related to the different wine quality. In order to minimize the soil variability, this work was conducted at a “within-vineyard” scale, comparing two similar soils (BRO11 and BRO12) previously identified with respect to pedological and hydrological properties within a single vineyard in Central Tuscany and that yielded highly contrasting wine quality upon cultivation of the same Sangiovese cultivar (BRO12 exhibited the higher quality). Our results showed an enrichment of Actinobacteria in BRO12, whereas Alfa- and Gamma-Proteobacteria were more abundant in BRO11, where an enrichment of bacteria involved in N fixation and denitrification occurred. Overall, the GeoChip output revealed a greater biological activity in BRO11 but a significant enrichment of sulfur-oxidation genes in BRO12 compared to BRO11 soil, where a higher level of arylsulfatase activity was also detected. Moreover, the low content of sulfates and available nitrogen found in BRO12 suggested that the reduced availability of sulfates for vine plants might limit the reduced glutathione (GSH) synthesis, which plays an important role in aroma protection in musts and wines. In conclusion, in addition to nitrogen availability, we propose that soil microbial sulfur metabolism may also play a key role in shaping plant physiology, grapes and wine quality. Overall, these results support the existence of a “microbial functional terroir” effect as a determining factor in vineyard-scale variation among wine grapes.

Distinct temporal diversity profiles for nitrogen cycling genes in a hyporheic microbiome.

Biodiversity is thought to prevent decline in community function in response to changing environmental conditions through replacement of organisms with similar functional capacity but different optimal growth characteristics. We examined how this concept translates to the within-gene level by exploring seasonal dynamics of within-gene diversity for genes involved in nitrogen cycling in hyporheic zone communities. Nitrification genes displayed low richness-defined as the number of unique within-gene phylotypes-across seasons. Conversely, denitrification genes varied in both richness and the degree to which phylotypes were recruited or lost. These results demonstrate that there is not a universal mechanism for maintaining community functional potential for nitrogen cycling activities, even across seasonal environmental shifts to which communities would be expected to be well adapted. As such, extreme environmental changes could have very different effects on the stability of the different nitrogen cycle activities. These outcomes suggest a need to modify existing conceptual models that link biodiversity to microbiome function to incorporate within-gene diversity. Specifically, we suggest an expanded conceptualization that 1) recognizes component steps (genes) with low diversity as potential bottlenecks influencing pathway-level function, and 2) includes variation in both the number of entities (e.g. species, phylotypes) that can contribute to a given process and the turnover of those entities in response to shifting conditions. Building these concepts into process-based ecosystem models represents an exciting opportunity to connect within-gene-scale ecological dynamics to ecosystem-scale services.

Nitrogen-cycling microbial community functional potential and enzyme activities in cultured biofilms with response to inorganic nitrogen availability.

Biofilms mediate crucial biochemical processes in aquatic ecosystems. It was hypothesized that eutrophication may promote the growth of biofilms, resulting in larger numbers of functional genes. However, the metabolic activity and the roles of biofilms in N cycling will be affected by ambient inorganic nitrogen availability, not by the abundance of functional genes. Biofilms were cultured either with replete inorganic nitrogen (N-rep) or without exogenous inorganic nitrogen supply (N-def) in a flow incubator, and the N-cycling gene abundances (nifH, N2 fixation; amoA, ammonia oxidation, archaea and bacteria; nirS and nirK, denitrification) and enzyme activities (nitrogenase and nitrate reductase) were analyzed. The results showed that, comparing the N-def and N-rep biofilms, the former contained lower nifH gene abundance, but higher nitrogenase activity (NA), while the latter contained higher nifH gene abundance, but lower NA. Different patterns of NA diel variations corresponded to the dynamic microbial community composition and different stages of biofilm colonization. Ammonia oxidizing bacteria (AOB), detected only in N-def biofilms, were responsible for nitrification in biofilms. N-rep biofilms contained high nirS and nirK gene abundance and high denitrification enzyme activity, but N-def biofilms contained significantly lower denitrification gene abundance and activity. In general, the strong N2 fixation in N-def biofilms and strong denitrification in N-rep biofilms assured the balance of aquatic ecosystems. The results suggested that evaluation of the functional processes of N cycling should not only focus on genetic potential, but also on the physiological activity of biofilms.

Bacterial Physiological Adaptations to Contrasting Edaphic Conditions Identified Using Landscape Scale Metagenomics.

ABSTRACTEnvironmental factors relating to soil pH are important regulators of bacterial taxonomic biodiversity, yet it remains unclear if such drivers affect community functional potential. To address this, we applied whole-genome metagenomics to eight geographically distributed soils at opposing ends of a landscape soil pH gradient (where “low-pH” is ~pH 4.3 and “high-pH” is ~pH 8.3) and evaluated functional differences with respect to functionally annotated genes. First, differences in taxonomic and functional diversity between the two pH categories were assessed with respect to alpha diversity (mean sample richness) and gamma diversity (total richness pooled for each pH category). Low-pH soils, also exhibiting higher organic matter and moisture, consistently had lower taxonomic alpha and gamma diversity, but this was not apparent in assessments of functional alpha and gamma diversity. However, coherent changes in the relative abundances of annotated genes between low- and high-pH soils were identified; with strong multivariate clustering of samples according to pH independent of geography. Assessment of indicator genes revealed that the acidic organic-rich soils possessed a greater abundance of cation efflux pumps, C and N direct fixation systems, and fermentation pathways, indicating adaptations to both acidity and anaerobiosis. Conversely, high-pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings highlight the distinctive physiological adaptations required for bacteria to survive in soils of various nutrient availability and edaphic conditions and more generally indicate that bacterial functional versatility with respect to functional gene annotations may not be constrained by taxonomy.

Effect of Water Chemistry and Hydrodynamics on Nitrogen Transformation Activity and Microbial Community Functional Potential in Hyporheic Zone Sediment Columns.

Hyporheic zones (HZ) are active biogeochemical regions where groundwater and surface water mix. N transformations in HZ sediments were investigated in columns with a focus on understanding how the dynamic changes in groundwater and surface water mixing affect microbial community and its biogeochemical function with respect to N transformations. The results indicated that denitrification, DNRA, and nitrification rates and products changed quickly in response to changes in water and sediment chemistry, fluid residence time, and groundwater-surface water exchange. These changes were accompanied by the zonation of denitrification functional genes along a 30 cm advective flow path after a total of 6 days' elution of synthetic groundwater with fluid residence time >9.8 h. The shift of microbial functional potential toward denitrification was correlated with rapid NO3- reduction collectively affected by NO3- concentration and fluid residence time, and was resistant to short-term groundwater-surface water exchange on a daily basis. The results implied that variations in microbial functional potential and associated biogeochemical reactions in the HZ may occur at space scales where steep concentration gradients present along the flow path and the variations would respond to dynamic HZ water exchange over different time periods common to natural and managed riverine systems.

Microbial Community Functional Potential and Composition Are Shaped by Hydrologic Connectivity in Riverine Floodplain Soils.

Riverine floodplains are ecologically and economically valuable ecosystems that are heavily threatened by anthropogenic stressors. Microbial communities in floodplain soils mediate critical biogeochemical processes, yet we understand little about the relationship between these communities and variation in hydrologic connectivity related to land management or topography. Here, we present metagenomic evidence that differences among microbial communities in three floodplain soils correspond to a long-term gradient of hydrologic connectivity. Specifically, all strictly anaerobic taxa and metabolic pathways were positively associated with increased hydrologic connectivity and flooding frequency. In contrast, most aerobic taxa and all strictly aerobic pathways were negatively related to hydrologic connectivity and flooding frequency. Furthermore, the genetic potential to metabolize organic compounds tended to decrease as hydrologic connectivity increased, which may reflect either the observed concomitant decline of soil organic matter or the parallel increase in both anaerobic taxa and pathways. A decline in soil N, accompanied by an increased genetic potential for oligotrophic N acquisition subsystems, suggests that soil nutrients also shape microbial communities in these soils. We conclude that differences among floodplain soil microbial communities can be conceptualized along a gradient of hydrologic connectivity. Additionally, we show that these differences are likely due to connectivity-related variation in flooding frequency, soil organic matter, and soil N. Our findings are particularly relevant to the restoration and management of microbially mediated biogeochemical processes in riverine floodplain wetlands.

Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil.

Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas.

Skin Microbiome Surveys Are Strongly Influenced by Experimental Design

Culture-independent studies to characterize skin microbiota are increasingly common, due in part to affordable and accessible sequencing and analysis platforms. Compared to culture-based techniques, DNA sequencing of the bacterial 16S ribosomal RNA (rRNA) gene or whole metagenome shotgun (WMS) sequencing provides more precise microbial community characterizations. Most widely used protocols were developed to characterize microbiota of other habitats (i.e., gastrointestinal) and have not been systematically compared for their utility in skin microbiome surveys. Here we establish a resource for the cutaneous research community to guide experimental design in characterizing skin microbiota. We compare two widely sequenced regions of the 16S rRNA gene to WMS sequencing for recapitulating skin microbiome community composition, diversity, and genetic functional enrichment. We show that WMS sequencing most accurately recapitulates microbial communities, but sequencing of hypervariable regions 1-3 of the 16S rRNA gene provides highly similar results. Sequencing of hypervariable region 4 poorly captures skin commensal microbiota, especially Propionibacterium. WMS sequencing, which is resource and cost intensive, provides evidence of a community's functional potential; however, metagenome predictions based on 16S rRNA sequence tags closely approximate WMS genetic functional profiles. This study highlights the importance of experimental design for downstream results in skin microbiome surveys.

Colonic bacterial composition in Parkinson's disease.

We showed that Parkinson's disease (PD) patients have alpha-synuclein (α-Syn) aggregation in their colon with evidence of colonic inflammation. If PD patients have altered colonic microbiota, dysbiosis might be the mechanism of neuroinflammation that leads to α-Syn misfolding and PD pathology. Sixty-six sigmoid mucosal biopsies and 65 fecal samples were collected from 38 PD patients and 34 healthy controls. Mucosal-associated and feces microbiota compositions were characterized using high-throughput ribosomal RNA gene amplicon sequencing. Data were correlated with clinical measures of PD, and a predictive assessment of microbial community functional potential was used to identify microbial functions. The mucosal and fecal microbial community of PD patients was significantly different than control subjects, with the fecal samples showing more marked differences than the sigmoid mucosa. At the taxonomic level of genus, putative, "anti-inflammatory" butyrate-producing bacteria from the genera Blautia, Coprococcus, and Roseburia were significantly more abundant in feces of controls than PD patients. Bacteria from the genus Faecalibacterium were significantly more abundant in the mucosa of controls than PD. Putative, "proinflammatory" Proteobacteria of the genus Ralstonia were significantly more abundant in mucosa of PD than controls. Predictive metagenomics indicated that a large number of genes involved in metabolism were significantly lower in the PD fecal microbiome, whereas genes involved in lipopolysaccharide biosynthesis and type III bacterial secretion systems were significantly higher in PD patients. This report provides evidence that proinflammatory dysbiosis is present in PD patients and could trigger inflammation-induced misfolding of α-Syn and development of PD pathology.

Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences.

Although the importance of viruses in natural ecosystems is widely acknowledged, the functional potential of viral communities is yet to be determined. Viral genomes are traditionally believed to carry only those genes that are directly pertinent to the viral life cycle, though this view was challenged by the discovery of metabolism genes in several phage genomes. Metagenomic approaches extended these analyses to a community scale, and several studies concluded that microbial and viral communities encompass similar functional potentials. However, these conclusions could originate from the presence of cellular DNA within viral metagenomes. We developed a computational method to estimate the proportion and origin of cellular sequences in a set of 67 published viromes. A quarter of the datasets were found to contain a substantial amount of sequences originating from cellular genomes. When considering only viromes with no cellular DNA detected, the functional potential of viral and microbial communities was found to be fundamentally different—a conclusion more consistent with the actual picture drawn from known viruses. Yet a significant number of cellular metabolism genes was still retrieved in these viromes, suggesting that the presence of auxiliary genes involved in various metabolic pathways within viral genomes is a general trend in the virosphere.