Bacterial evolution: Genomics of metabolic trade-offs

A general pattern of plant traits and their relationships with environmental factors and microbial life-history strategies

The trait-based unidimensional plant economics spectrum provides a valuable framework for understanding plant adaptation strategies to the environment. However, it is still uncertain whether there is a general multidimensionality of how variation of both leaf and fine root traits are influenced by environmental factors, and how these relate to microbial resource strategies. Here, we examined the coordination patterns of four pairs of similar leaf and fine root traits of herbaceous plants in an alpine meadow at the community-level, and their environmental driving patterns. We then assessed their correlation with microbial life-history strategies, as these exhibit analogous resource strategies with plants in terms of growth and resource utilization efficiency. Results exhibited an analogous multidimensionality of the economics spectrum for leaf and fine root traits: the first dimension, collaboration gradient, primarily represented a tradeoff between lifespan and resource foraging efficiency; the second dimension, conservation gradient, primarily represented a tradeoff between conservation and acquisition in resource uptake. Climate variables had a stronger impact on both dimensions for leaf and fine root traits than soil variables did; whereas, the primary drivers were more complex for fine root traits than for leaf traits. The collaboration gradient of leaf and fine root traits exhibited consistent relationships with soil microbial life-history strategies, both showed negative and positive correlation with bacterial and fungal strategies, respectively. Our findings suggest that both leaves and fine roots have general multidimensional strategies for adapting to new environments and provide a solid basis for further understanding the relationships between the adaptive strategies of plants and microbes.

Enhanced AHL-mediated quorum sensing accelerates the start-up of biofilm reactors by elevating the fitness of fast-growing bacteria in sludge and biofilm communities

Quorum sensing (QS)-based manipulations emerge as a promising solution for biofilm reactors to overcome challenges from inefficient biofilm formation and lengthy start-ups. However, the ecological mechanisms underlying how QS regulates microbial behaviors and community assembly remain elusive. Herein, by introducing different levels of N-acyl-homoserine lactones, we manipulated the strength of QS during the start-up of moving bed biofilm reactors and compared the dynamics of bacterial communities. We found that enhanced QS elevated the fitness of fast-growing bacteria with high ribosomal RNA operon (rrn) copy numbers in their genomes in both the sludge and biofilm communities. This led to notably increased extracellular substance production, as evidenced by strong positive correlations between community-level rrn copy numbers and extracellular proteins and polysaccharides (Pearson's r = 0.529-0.830, P < 0.001). Network analyses demonstrated that enhanced QS significantly promoted the ecological interactions among taxa, particularly cooperative interactions. Bacterial taxa with higher network degrees were more strongly correlated with extracellular substances, suggesting their crucial roles as public goods in regulating bacterial interactions and shaping network structures. However, the assembly of more cooperative communities in QS-enhanced reactors came at the cost of decreased network stability and modularity. Null model and dissimilarity-overlap curve analysis revealed that enhanced QS strengthened stochastic processes in community assembly and rendered the universal population dynamics more convergent. Additionally, these shaping effects were consistent for both the sludge and biofilm communities, underpinning the planktonic-to-biofilm transition. This work highlights that QS manipulations efficiently drive community assembly and confer specialized functional traits to communities by recruiting taxa with specific life strategies and regulating interspecific interactions. These ecological insights deepen our understanding of the rules governing microbial societies and provide guidance for managing engineering ecosystems.

Community stability of free-living and particle-attached bacteria in a subtropical reservoir with salinity fluctuations over 3 years

Changes in salinity have a profound influence on ecological services and functions of inland freshwater ecosystems, as well as on the shaping of microbial communities. Bacterioplankton, generally classified into free-living (FL) and particle-attached (PA) forms, are main components of freshwater ecosystems and play key functional roles for biogeochemical cycling and ecological stability. However, there is limited knowledge about the responses of community stability of both FL and PA bacteria to salinity fluctuations. Here, we systematically explored changes in community stability of both forms of bacteria based on high-frequency sampling in a shallow urban reservoir (Xinglinwan Reservoir) in subtropical China for 3 years. Our results indicated that (1) salinity was the strongest environmental factor determining FL and PA bacterial community compositions - rising salinity increased the compositional stability of both bacterial communities but decreased their α-diversity. (2) The community stability of PA bacteria was significantly higher than that of FL at high salinity level with low salinity variance scenarios, while the opposite was found for FL bacteria, i.e., their stability was higher than PA bacteria at low salinity level with high variance scenarios. (3) Both bacterial traits (e.g., bacterial genome size and interaction strength of rare taxa) and precipitation-induced factors (e.g., changes in salinity and particle) likely contributed collectively to differences in community stability of FL and PA bacteria under different salinity scenarios. Our study provides additional scientific basis for ecological management, protection and restoration of urban reservoirs under changing climatic and environmental conditions.

Land use, stratified wastewater and sediment, and microplastic attribute factors jointly influence the microplastic prevalence and bacterial colonization patterns in sewer habitats

The capacity of microplastics to harbor and propagate bacteria has been the focus of attention over the last decade. Such microplastic-supported bacterial colonization behavior in the municipal sewer system could be a critical ecological link influencing the biogeochemical activities and risks in receiving waters in urban areas, given the alarming microplastic loads discharged there. This study conducted a large-scale survey covering a wide range of residential and industrial catchments in Shanghai, China. We aimed to assess the microplastic prevalence and bacterial colonization patterns in different sewer habitats and to explore the role of land use, stratified wastewater and sediment, and microplastic attributes in shaping the patterns. We found that the sewer system formed a temporal but pronounced microplastic pool, with land use playing a significant role in the variability of microplastic prevalence. Industrial sewers contained a high abundance of microplastics with large particle sizes, diverse polymer compositions, and shapes. However, while there was a spatial discrepancy between urban and suburban areas in the abundance of microplastics in residential sewers, their predominant polymer and shape types were simple, i.e., polyethylene terephthalate (PET) and fibers. Sewer habitat characteristics, particularly the stratified wastewater and sediment determined microbial colonization patterns. The latter acted as a long-term sink for microplastics and supported the high growth of colonizers. In contrast, the wastewater plastisphere presented novel niches, hosting communities with a marked proportion of unique bacterial genera after colonization. Besides, statistics showed a highly positive and dense co-occurrence network of the plastisphere communities, especially those from the industrial sewer sediment, with enhanced metabolic activity, cellular processes and systems, and increased human pathogenic potential. Findings indicated a coarse and uncertain effect of the selective pressure of microplastic attributes on plastisphere community structure differentiation.

High-throughput absolute quantification sequencing reveals the adaptive succession and assembly pattern of plastisphere communities in municipal sewer systems: Influence of environmental factors and microplastic polymer types

Municipal sewer systems have received increasing attention due to the magnitude of the microplastic stock and its potential ecological impacts. However, as a critical aspect of the adverse impacts, little is known about the plastisphere that forms in these engineered environments. Using high-throughput absolute quantification sequencing, we conducted a systemic study combining field survey and laboratory batch test to explain the general plastisphere pattern and the role of environmental and polymeric factors in driving plastisphere succession and assembly there. We demonstrated the capacity of microplastics to support high levels of microbial colonization, increasing by 8.7-56.0 and 1.26-5.62 times at field and laboratory scales, respectively, despite the less diverse communities hosted in the resulting plastisphere. Sediment communities exhibited higher diversity but greater loss of specific operational taxonomic units in their plastisphere than in the wastewater. The former plastisphere had primarily an enhanced methanogenesis-oriented metabolic network linked to hydrolysis fermentation, hydrogen-producing acetogenesis, and denitrification, while the latter had a pronounced niche partitioning and competitive interaction network. Exogenous substrate flux and composition were key in stimulating plastisphere community growth and succession. Furthermore, the high nitrogen baseline facilitated alternative niche formation for plastisphere nitrifiers and denitrifiers, and the plastisphere pathogens associated with denitrification and plastic biodegradation functions increased significantly. The aerobic state also promoted a 1.71 times higher colonizer load and a denser interaction pattern than the anaerobic state. Selective filtering by polymers was evident: polyethylene supported higher plastisphere diversity than polypropylene. This study provides new insights into the mechanisms driving colonizer loads and the adaptive succession and assembly of the plastisphere in such a typically hydrodynamic and highly contaminated environment. The results help to fill the knowledge gap in understanding the potential role of microplastics in shaping the microecology of sewers and increasing health risks and substrate loss during sewer transfer.

Enhanced permeation performance of biofiltration-facilitated gravity-driven membrane (GDM) systems by in-situ application of UV and VUV: Comprehensive insights from thermodynamic and multi-omics perspectives

Biofouling is a major challenge limiting the practical application of biofiltration-facilitated gravity-driven membrane (GDM) systems in drinking water treatment. In this study, ultraviolet irradiation, including ultraviolet (UV) and vacuum ultraviolet (VUV) irradiation, was used for in-situ purification of membrane tanks to control membrane biofouling. After using UV and VUV, the permeate flux increased significantly by 26.1% and 78.3%, respectively, which was mainly due to the decreased cake layer resistance (Rc). The permeability of the biofouling layer improved after UV and VUV application, as evidenced by the increased surface porosity and decreased thickness. The contents of loosely bound extracellular proteins (LB-PN) and tightly bound extracellular proteins (TB-PN) in the biofouling layer were reduced after UV and VUV irradiation. The decreased LB-PN and TB-PN improved the interfacial free energy between the fouling itself and between the fouling and the membrane, which contributed to the reduction of interfacial cohesion and adhesion, resulting in a looser and thinner biofouling layer and a cleaner membrane. The concentration of protein-like material in the membrane tank decreased after UV and VUV irradiation, significantly altering the bacterial community structure on the membrane surface (Mantel's r > 0.7, p < 0.05). The changes in the metabolic state were responsible for the differences in the LB-PN and TB-PN contents. The inhibition of "Alanine, aspartate and glutamate metabolism" and "Glycine, serine and threonine metabolism" reduced amino acid biosynthesis, which restricted the secretion of LB-PN and TB-PN. Critical genera in the Proteobacteria phylum, such as Hirschia, Rhodobacter, Nordella, Candidatus_Berkiella, and Limnohabitans, were involved in metabolite transformation. Overall, the in-situ application of UV and VUV can be an effective alternative strategy to mitigate membrane biofouling, which would facilitate the practical application of biofiltration-facilitated GDM systems in drinking water treatment.

Photo-aging promotes the inhibitory effect of polystyrene microplastics on microbial reductive dechlorination of a polychlorinated biphenyl mixture (Aroclor 1260)

Polychlorinated biphenyls (PCBs) and microplastics (MPs) commonly co-exist in various environments. MPs inevitably start aging once they enter environment. In this study, the effect of photo-aged polystyrene MPs on microbial PCB dechlorination was investigated. After a UV aging treatment, the proportion of oxygen-containing groups in MPs increased. Photo-aging promoted the inhibitory effect of MPs on microbial reductive dechlorination of PCBs, mainly attributed to the inhibition of meta-chlorine removal. The inhibitory effects on hydrogenase and adenosine triphosphatase activity by MPs increased with increasing aging degree, which may be attributed to electron transfer chain inhibition. PERMANOVA showed significant differences in microbial community structure between culturing systems with and without MPs (p < 0.05). Co-occurrence network showed a simpler structure and higher proportion of negative correlation in the presence of MPs, especially for biofilms, resulting in increased potential for competition among bacteria. MP addition altered microbial community diversity, structure, interactions, and assembly processes, which was more deterministic in biofilms than in suspension cultures, especially regarding the bins of Dehalococcoides. This study sheds light on the microbial reductive dechlorination metabolisms and mechanisms where PCBs and MPs co-exist and provides theoretical guidance for in situ application of PCB bioremediation technology.

Deciphering the distinct successional patterns and potential roles of abundant and rare microbial taxa of urban riverine plastisphere

Microbial colonization on microplastics has provoked global concern; however, many studies have not considered the successional patterns and potential roles of abundant and rare taxa of the plastisphere during colonization. Hence, we investigate the taxonomic composition, assembly, interaction and function of abundant and rare taxa in the riverine plastisphere by conducting microcosm experiments. Results showed that rare taxa occupied significantly high community diversity and niche breadth than the abundant taxa, which implies that rare taxa are essential components in maintaining the community stability of the plastisphere. However, the abundant taxa played a major role in driving the succession of plastisphere communities during colonization. Both stochastic and deterministic processes signally affected the plastisphere community assemblies; while, the deterministic patterns (heterogeneous selection) were especially pronounced for rare biospheres. Plastisphere microbial networks were shaped by the enhancement of network modularity and reinforcement of positive interactions. Rare taxa played critical roles in shaping stable plastisphere by occupying the key status in microbial networks. The strong interaction of rare and non-rare taxa suggested that multi-species collaboration might be conducive to the formation and stability of the plastisphere. Both abundant and rare taxa were enriched with plentiful functional genes related to carbon, nitrogen, phosphorus and sulfur cycling; however, their potential metabolic functions were significantly discrepant, implying that the abundant and rare microbes may play different roles in ecosystems. Overall, this study strengthens our comprehending of the mechanisms regarding the formation and maintenance of the plastisphere.

Collective decision-making in Pseudomonas aeruginosa involves transient segregation of quorum-sensing activities across cells

A hallmark of bacterial sociality is that groups can coordinate cooperative actions through a cell-to-cell communication process called quorum sensing (QS). QS regulates key bacterial phenotypes such as virulence in infections and digestion of extracellular compounds in the environment. Although QS responses are typically studied as group-level phenotypes, it is unclear whether individuals coordinate their actions at the single-cell level or whether group phenotypes simply reflect the sum of their noisy members. Here, we studied the behavior of Pseudomonas aeruginosa individuals by tracking their temporal commitments to the two intertwined Las and Rhl-QS systems, from low to high population density. Using chromosomally integrated fluorescent gene reporters, we found that QS gene expression (signal, receptor, and cooperative exoproduct) was noisy with heterogeneity peaking during the build-up phase of QS. Moreover, we observed the formation of discrete subgroups of cells that transiently segregate into two gene expression states: low Las-receptor expressers that instantly activate exoproduct production and high Las-receptor expressers with delayed exoproduct production. Later, gene expression activities converged with all cells fully committing to QS. We developed general mathematical models to show that gene expression segregation can mechanistically be spurred by molecular resource limitations during the initiation phase of regulatory cascades such as QS. Moreover, our models indicate that gene expression segregation across cells can operate as a built-in brake enabling a temporary bet-hedging strategy in unpredictable environments. Altogether, our work reveals that studying the behavior of bacterial individuals is key to understanding emergent collective actions at the group level.

Microbial life strategy with high rRNA operon copy number facilitates the energy and nutrient flux in anaerobic digestion

Microbial life strategy, reflected by rRNA operon (rrn) copy number, determines microbial ecological roles. However, the relationship between microbial life strategy and the energy and nutrient flux in anaerobic digestion (AD) remains elusive. This study investigated microbial rrn copy number and expression ratio using amplicon sequencing of 16S rRNA gene and 16S rRNA, and monitored CH₄ daily production to approximate the status of energy and nutrient flux in semi-continuous AD. A significantly positive correlation between the mean rrn copy number of microbial communities in digestate and CH₄ daily production was detected in the control treatment fed swine manure. The reduced feedstock complexity, by replacing parts of swine manure with fructose or apple waste, weakened the correlation. When feedstock complexity was increased again, the correlation was strengthened again. Similar results were detected in mean rrn expression ratio of microbial communities. The responses of mean rrn copy number and expression ratio of communities to feedstock addition differed between the reduced feedstock complexity and the control treatment, as well as between in digestate and in straw. Our findings reveal a novel relationship between microbial community life strategy and the energy and nutrient flux, and the roles of feedstock characteristics therein in AD.

Tracking the upstream history of aquatic microbes in a boreal lake yields new insights on microbial community assembly

Bacterial community structure can change rapidly across short spatial and temporal scales as environmental conditions vary, but the mechanisms underlying those changes are still poorly understood. Here, we assessed how a lake microbial community assembles by following its reorganization from the main tributary, which, when flowing into the lake, first traverses an extensive macrophyte-dominated vegetated habitat, before reaching the open water. Environmental conditions in the vegetated habitat changed drastically compared to both river and lake waters and represented a strong environmental gradient for the incoming bacteria. We used amplicon sequencing of the 16S rRNA gene and transcript to reconstruct the shifts in relative abundance of individual taxa and link this to their pattern in activity (here assessed with RNA:DNA ratios). Our results indicate that major shifts in relative abundance were restricted mostly to rare taxa (<0.1% of relative abundance), which seemed more responsive to environmental changes. Dominant taxa (>1% of relative abundance), on the other hand, traversed the gradient mostly unchanged with relatively low and stable RNA:DNA ratios. We also identified a high level of local recruitment and a seedbank of taxa capable of activating/inactivating, but these were almost exclusively associated with the rare biosphere. Our results suggest a scenario where the lake community results from a reshuffling of the rank abundance structure within the incoming rare biosphere, driven by selection and growth, and that numerical dominance is not a synonym of activity, growth rate, or environmental selection, but rather reflect mass effects structuring these freshwater bacterial communities.

Substrate Utilization and Competitive Interactions Among Soil Bacteria Vary With Life-History Strategies

Microorganisms have evolved various life-history strategies to survive fluctuating resource conditions in soils. However, it remains elusive how the life-history strategies of microorganisms influence their processing of organic carbon, which may affect microbial interactions and carbon cycling in soils. Here, we characterized the genomic traits, exometabolite profiles, and interactions of soil bacteria representing copiotrophic and oligotrophic strategists. Isolates were selected based on differences in ribosomal RNA operon (rrn) copy number, as a proxy for life-history strategies, with pairs of “high” and “low” rrn copy number isolates represented within the Micrococcales, Corynebacteriales, and Bacillales. We found that high rrn isolates consumed a greater diversity and amount of substrates than low rrn isolates in a defined growth medium containing common soil metabolites. We estimated overlap in substrate utilization profiles to predict the potential for resource competition and found that high rrn isolates tended to have a greater potential for competitive interactions. The predicted interactions positively correlated with the measured interactions that were dominated by negative interactions as determined through sequential growth experiments. This suggests that resource competition was a major force governing interactions among isolates, while cross-feeding of metabolic secretion likely contributed to the relatively rare positive interactions observed. By connecting bacterial life-history strategies, genomic features, and metabolism, our study advances the understanding of the links between bacterial community composition and the transformation of carbon in soils.

Turnover in Life-Strategies Recapitulates Marine Microbial Succession Colonizing Model Particles

Particulate organic matter (POM) in the ocean sustains diverse communities of bacteria that mediate the remineralization of organic complex matter. However, the variability of these particles and of the environmental conditions surrounding them present a challenge to the study of the ecological processes shaping particle-associated communities and their function. In this work, we utilize data from experiments in which coastal water communities are grown on synthetic particles to ask which are the most important ecological drivers of their assembly and associated traits. Combining 16S rRNA amplicon sequencing with shotgun metagenomics, together with an analysis of the full genomes of a subset of isolated strains, we were able to identify two-to-three distinct community classes, corresponding to early vs. late colonizers. We show that these classes are shaped by environmental selection (early colonizers) and facilitation (late colonizers) and find distinctive traits associated with each class. While early colonizers have a larger proportion of genes related to the uptake of nutrients, motility, and environmental sensing with few pathways enriched for metabolism, late colonizers devote a higher proportion of genes for metabolism, comprising a wide array of different pathways including the metabolism of carbohydrates, amino acids, and xenobiotics. Analysis of selected pathways suggests the existence of a trophic-chain topology connecting both classes for nitrogen metabolism, potential exchange of branched chain amino acids for late colonizers, and differences in bacterial doubling times throughout the succession. The interpretation of these traits suggests a distinction between early and late colonizers analogous to other classifications found in the literature, and we discuss connections with the classical distinction between r- and K-strategists.

Eco-evolutionary responses of the microbial loop to surface ocean warming and consequences for primary production

Predicting the response of ocean primary production to climate warming is a major challenge. One key control of primary production is the microbial loop driven by heterotrophic bacteria, yet how warming alters the microbial loop and its function is poorly understood. Here we develop an eco-evolutionary model to predict the physiological response and adaptation through selection of bacterial populations in the microbial loop and how this will impact ecosystem function such as primary production. We find that the ecophysiological response of primary production to warming is driven by a decrease in regenerated production which depends on nutrient availability. In nutrient-poor environments, the loss of regenerated production to warming is due to decreasing microbial loop activity. However, this ecophysiological response can be opposed or even reversed by bacterial adaptation through selection, especially in cold environments: heterotrophic bacteria with lower bacterial growth efficiency are selected, which strengthens the "link" behavior of the microbial loop, increasing both new and regenerated production. In cold and rich environments such as the Arctic Ocean, the effect of bacterial adaptation on primary production exceeds the ecophysiological response. Accounting for bacterial adaptation through selection is thus critically needed to improve models and projections of the ocean primary production in a warming world.

The Microbial Mechanisms of a Novel Photosensitive Material (Treated Rape Pollen) in Anti-Biofilm Process under Marine Environment

Marine biofouling is a worldwide problem in coastal areas and affects the maritime industry primarily by attachment of fouling organisms to solid immersed surfaces. Biofilm formation by microbes is the main cause of biofouling. Currently, application of antibacterial materials is an important strategy for preventing bacterial colonization and biofilm formation. A natural three-dimensional carbon skeleton material, TRP (treated rape pollen), attracted our attention owing to its visible-light-driven photocatalytic disinfection property. Based on this, we hypothesized that TRP, which is eco-friendly, would show antifouling performance and could be used for marine antifouling. We then assessed its physiochemical characteristics, oxidant potential, and antifouling ability. The results showed that TRP had excellent photosensitivity and oxidant ability, as well as strong anti-bacterial colonization capability under light-driven conditions. Confocal laser scanning microscopy showed that TRP could disperse pre-established biofilms on stainless steel surfaces in natural seawater. The biodiversity and taxonomic composition of biofilms were significantly altered by TRP (p < 0.05). Moreover, metagenomics analysis showed that functional classes involved in the antioxidant system, environmental stress, glucose−lipid metabolism, and membrane-associated functions were changed after TRP exposure. Co-occurrence model analysis further revealed that TRP markedly increased the complexity of the biofilm microbial network under light irradiation. Taken together, these results demonstrate that TRP with light irradiation can inhibit bacterial colonization and prevent initial biofilm formation. Thus, TRP is a potential nature-based green material for marine antifouling.

Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities

Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (rrn) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a “hunger games” hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability.

Environmental and biotic factors control ecological communities. Here, the authors study community ribosomal rRNA gene copy number in coastal sediment and ocean bacterial communities, and in microcosm nutrient addition experiments, to propose a conceptual framework of how nutrient supply and ecological interactions shape the community.

The structure and assembly mechanisms of plastisphere microbial community in natural marine environment

The microbial colonization profiles on microplastics (MPs) in marine environments have recently sparked global interest. However, many studies have characterized plastisphere microbiomes without considering the ecological processes that underly microbiome assembly. Here, we carried out a three-timepoint exposure experiment at 1-, 4-, and 8-week and investigated the colonization dynamics for polyethylene, polypropylene, polystyrene, polyvinyl chloride, and acrylonitrile-butadiene-styrene MP pellets in natural coastal water. Using high-throughput sequencing of 16S rRNA, we found diversity and evenness were higher (p < 0.05) in the plastisphere communities than those in seawater, and microorganisms colonizing were co-influenced by environmental factors, polymer types, and exposure duration. Functional potential and co-occurrence network analysis revealed that MP exposure enriched the xenobiotic biodegradation potential and reduced the complexity of the MP microbial network. Simultaneously, null-model analyses indicated that stochastic processes contributed a bigger role than deterministic processes in shaping plastisphere microbial community structure with dispersal limitations contributing to a greater extent to microbial succession trajectories. These results implied the plastic surface had a more important role as a raft onto which microbes attach rather than selectively recruiting plastic-specific microbial colonizers. Our work strengthened the understanding of the ecological mechanisms by which microbial community patterns are controlled during colonization by plastic-associated microbes.

Strategic traits of bacteria and archaea vary widely within substrate-use groups

Quantitative traits such as maximum growth rate and cell radial diameter are one facet of ecological strategy variation across bacteria and archaea. Another facet is substrate-use pathways, such as iron reduction or methylotrophy. Here, we ask how these two facets intersect, using a large compilation of data for culturable species and examining seven quantitative traits (genome size, signal transduction protein count, histidine kinase count, growth temperature, temperature-adjusted maximum growth rate, cell radial diameter and 16S rRNA operon copy number). Overall, quantitative trait variation within groups of organisms possessing a particular substrate-use pathway was very broad, outweighing differences between substrate-use groups. Although some substrate-use groups had significantly different means for some quantitative traits, standard deviation of quantitative trait values within each substrate-use pathway mostly averaged between 1.6 and 1.8 times larger than standard deviation across group means. Most likely, this wide variation reflects ecological strategy: for example, fast maximum growth rate is likely to express an early successional or copiotrophic strategy, and maximum growth varies widely within most substrate-use pathways. In general, it appears that these quantitative traits express different and complementary information about ecological strategy, compared with substrate use.

Metabolic patterns reveal enhanced anammox activity at low nitrogen conditions in the integrated I-ABR

Substrate concentrations greatly influence bacterial growth and metabolism. However, optimal nitrogen concentrations for anammox bacteria in nitrogen-limited environments remain unclear. Here, we observed enhanced nitrogen metabolism and anabolism of anammox bacteria at low nitrogen conditions. Efficient nitrogen removal was achieved at ammonium and nitrite influent concentration of 30 mg/L under HRT of 1 hr, with an average nitrogen removal rate (NRR) of 0.73 kg N/(m³ ·day) in I-ABR composed of four compartments. The highest anammox activity of 6.25 mmol N/ (gVSS·hr) was observed in the fourth compartment (C4) with the lowest substrate levels (ammonium and nitrite of 11.6 mg/L and 7 mg/L). This could be resulted from the highest expression level of genes involved in nitrogen metabolism in C4, which was 1.49-1.67 times higher than that in other compartments. Besides, the second compartment (C2) exhibited the most active anabolism at ammonium and nitrite of 17 mg/L and 13 mg/L, respectively, which contributed to the most active amino acid synthesis and thus the highest EPS (1.35 times higher) in C2. This enhanced amino acid auxotrophy between anammox bacteria with heterotrophs, and consequently, heterotrophs thrived and competed for nitrite. These results hint at the potential application of anammox process in micro-polluted water. PRACTITIONER POINTS: High nitrogen removal and efficient biomass retention at low nitrogen concentrations under short HRT was achieved in I-ABR. Optimal concentrations for anammox nitrogen removal and anabolism were discussed under low nitrogen concentrations. More active anabolism contributed to enhanced amino acid synthesis and thus higher EPS contents. Low substrate levels led to enhanced expression of genes involved in nitrogen metabolism and thus high anammox activity.

Distinct growth stages controlled by the interplay of deterministic and stochastic processes in functional anammox biofilms

Mainstream anaerobic ammonium oxidation (anammox) represents one of the most promising energy-efficient mechanisms of fixed nitrogen elimination from wastewaters. However, little is known about the exact processes and drivers of microbial community assembly within the complex microbial biofilms that support anammox in engineered ecosystems. Here, we followed anammox biofilm development on fresh carriers in an established 8m³ mainstream anammox reactor that is exposed to seasonal temperature changes (~25-12°C) and varying NH₄⁺ concentrations (5-25 mg/L). We use fluorescence in situ hybridization and 16S rRNA gene sequencing to show that three distinct stages of biofilm development emerge naturally from microbial community composition and biofilm structure. Neutral modelling and network analysis are employed to elucidate the relative importance of stochastic versus deterministic processes and synergistic and antagonistic interactions in the biofilms during their development. We find that the different phases are characterized by a dynamic succession and an interplay of both stochastic and deterministic processes. The observed growth stages (Colonization, Succession and Maturation) appear to be the prerequisite for the anticipated growth of anammox bacteria and for reaching a biofilm community structure that supports the desired metabolic and functional capacities observed for biofilm carriers already present in the system (~100g_NH4-N m³ d^-1). We discuss the relevance of this improved understanding of anammox-community ecology and biofilm development in the context of its practical application in the start-up, configuration, and optimization of anammox biofilm reactors.

Microbial debromination of hexabromocyclododecanes

Hexabromocyclododecanes (HBCDs), a new sort of brominated flame retardants (BFRs), are globally prevalent and recalcitrant toxic environmental pollutants. HBCDs have been found in many environmental media and even in the human body, leading to serious health concerns. HBCDs are biodegradable in the environment. By now, dozens of bacteria have been discovered with the ability to transform HBCDs. Microbial debromination of HBCDs is via HBr-elimination, HBr-dihaloelimination, and hydrolytic debromination. Biotic transformation of HBCDs yields many hydroxylated and lower brominated compounds which lack assessment of ecological toxicity. Bioremediation of HBCD pollution has only been applied in the laboratory. Here, we review the current knowledge about microbial debromination of HBCDs, aiming to promote the bioremediation applied in HBCD contaminated sites. KEY POINTS: • Microbial debromination of HBCDs is via hydrolytic debromination, HBr-elimination, and HBr-dihaloelimination. • Newly occurred halogenated contaminants such as HBCDs hitch the degradation pathway tamed by previously discharged anthropogenic organohalides. • Strategy that combines bioaugmentation with phytoremediation for bioremediation of HBCD pollution is promising.

Ralstonia solanacearum Depends on Catabolism of Myo-Inositol, Sucrose, and Trehalose for Virulence in an Infection Stage-Dependent Manner

The soilborne pathogen Ralstonia solanacearum causes a lethal bacterial wilt disease of tomato and many other crops by infecting host roots, then colonizing the water-transporting xylem vessels. Tomato xylem sap is nutritionally limiting but it does contain some carbon sources, including sucrose, trehalose, and myo-inositol. Transcriptomic analyses revealed that R. solanacearum expresses distinct catabolic pathways at low cell density (LCD) and high cell density (HCD). To investigate the links between bacterial catabolism, infection stage, and virulence, we measured in planta fitness of bacterial mutants lacking specific carbon catabolic pathways expressed at either LCD or HCD. We hypothesized that early in disease, during root infection, the bacterium depends on carbon sources catabolized at LCD, while HCD carbon sources are only required later in disease during stem colonization. A R. solanacearum ΔiolG mutant unable to use the LCD-catabolized nutrient myo-inositol was defective in tomato root colonization, but after it reached the stem this strain colonized and caused symptoms as well as wild type. In contrast, R. solanacearum mutants unable to use the HCD-catabolized nutrients sucrose (ΔscrA), trehalose (ΔtreA), or both (ΔscrA/treA), infected roots as well as wild-type R. solanacearum but were defective in colonization and competitive fitness in midstems and had reduced virulence. Further, xylem sap from tomato plants colonized by ΔscrA, ΔtreA, or ΔscrA/treA R. solanacearum mutants contained twice as much sucrose as sap from plants colonized by wild-type R. solanacearum. Together, these findings suggest that quorum sensing specifically adapts R. solanacearum metabolism for success in the different nutritional environments of plant roots and xylem sap.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Cell size, genome size, and maximum growth rate are near-independent dimensions of ecological variation across bacteria and archaea

Among bacteria and archaea, maximum relative growth rate, cell diameter, and genome size are widely regarded as important influences on ecological strategy. Via the most extensive data compilation so far for these traits across all clades and habitats, we ask whether they are correlated and if so how. Overall, we found little correlation among them, indicating they should be considered as independent dimensions of ecological variation. Nor was correlation evident within particular habitat types. A weak nonlinearity (6% of variance) was found whereby high maximum growth rates (temperature-adjusted) tended to occur in the midrange of cell diameters. Species identified in the literature as oligotrophs or copiotrophs were clearly separated on the dimension of maximum growth rate, but not on the dimensions of genome size or cell diameter.

Trait dimensions in bacteria and archaea compared to vascular plants

Bacteria and archaea have very different ecology compared to plants. One similarity, though, is that much discussion of their ecological strategies has invoked concepts such as oligotrophy or stress tolerance. For plants, so-called 'trait ecology'-strategy description reframed along measurable trait dimensions-has made global syntheses possible. Among widely measured trait dimensions for bacteria and archaea three main axes are evident. Maximum growth rate in association with rRNA operon copy number expresses a rate-yield trade-off that is analogous to the acquisitive-conservative spectrum in plants, though underpinned by different trade-offs. Genome size in association with signal transduction expresses versatility. Cell size has influence on diffusive uptake and on relative wall costs. These trait dimensions, and potentially others, offer promise for interpreting ecology. At the same time, there are very substantial differences from plant trait ecology. Traits and their underpinning trade-offs are different. Also, bacteria and archaea use a variety of different substrates. Bacterial strategies can be viewed both through the facet of substrate-use pathways, and also through the facet of quantitative traits such as maximum growth rate. Preliminary evidence shows the quantitative traits vary widely within substrate-use pathways. This indicates they convey information complementary to substrate use.

Deciphering bacterial social traits via diffusible signal factor (DSF) -mediated public goods in an anammox community

Both the benefits of bacterial quorum sensing (QS) and cross-feeding for bio-reactor performance in wastewater treatment have been recently reported. As the social traits of microbial communities, how bacterial QS regulating bacterial trade-off by cross-feeding remains unclear. Here, we find diffusion signal factor (DSF), a kind of QS molecules, can bridge bacterial interactions through regulating public goods (extracellular polymeric substances (EPS), amino acids) for metabolic cross-feedings. It showed that exogenous DSF-addition leads to change of public goods level and community structure dynamics in the anammox consortia. Approaches involving meta-omics clarified that anammox and a Lautropia-affiliated species in the phylum Proteobacteria can supply costly public goods for DSF-Secretor species via secondary messenger c-di-GMP regulator (Clp) after sensing DSF. Meanwhile, DSF-Secretor species help anammox bacteria scavenge extracellular detritus, which creates a more suitable environment for the anammox species, enhances the anammox activity, and improves the nitrogen removal rate of anammox reactor. The trade-off induces discrepant metabolic loads of different microbial clusters, which were responsible for the community succession. It illustrated the potential to artificially alleviate metabolic loads for certain bacteria. Deciphering microbial interactions via QS not only provides insights for understanding the social behavior of microbial community, but also creates new thought for enhancing treatment performance through regulating bacterial social traits via quorum sensing-mediated public goods.

Deammonification process in municipal wastewater treatment: Challenges and perspectives

The deammonification process has been proved to be an efficient nitrogen removal process in treating high NH₄⁺-N concentration wastewater (sidestream deammonification). It is very hopeful to bring WWTP close to energy autarky. However, the feasibility of applying mainstream deammonification to sewage treatment need to be further explored. Therefore, this review attempts to give an overview of challenges in applying mainstream deammonification and to discuss the impacts of unfavorable conditions on main functional species. In addition, some novel control strategies to maintain the dominant position of desired species were summarized. Efficient solution to the conflict between AnAOB (Anaerobic ammonium-oxidizing bacteria) biomass retention and NOB (Nitrite oxidizing bacteria) wash out was also reviewed. Ultimately, we suggested further studies including effective improved process that achieve combination of autotrophy and organotrophy species based on the metabolic diversity of AnAOB.

Dynamics of coastal bacterial community average ribosomal RNA operon copy number reflect its response and sensitivity to ammonium and phosphate

The nutrient-rich effluent from wastewater treatment plants (WWTPs) constitutes a significant disturbance to coastal microbial communities, which in turn affect ecosystem functioning. However, little is known about how such disturbance could affect the community's stability, an important knowledge gap for predicting community response to future disturbances. Here, we examined dynamics of coastal sediment microbial communities with and without a history of WWTP's disturbances (named H1 and H0 hereafter) after simulated nutrient input loading at the low level (5 mg L^-1 NH₄⁺-N and 0.5 mg L^-1 PO₄^3--P) or high level (50 mg L^-1 NH₄⁺-N and 5.0 mg L^-1 PO₄^3--P) for 28 days. H0 community was highly sensitive to both low and high nutrient loading, showing a faster community turnover than H1 community. In contrast, H1 community was more efficient in nutrient removal. To explain it, we found that H1 community constituted more abundant and diversified r-strategists, known to be copiotrophic and fast in growth and reproduction, than H0 community. As nutrient was gradually consumed, both communities showed a succession of decreasing r-strategists. Accordingly, there was a decrease in community average ribosomal RNA operon (rrn) copy number, a recently established functional trait of r-strategists. Remarkably, the average rrn copy number of H0 communities was strongly correlated with NH₄⁺-N (R² = 0.515, P = 0.009 for low nutrient loading; R² = 0.749, P = 0.001 for high nutrient loading) and PO₄^3--P (R² = 0.378, P = 0.034 for low nutrient loading; R² = 0.772, P = 0.001 for high nutrient loading) concentrations, while that of H1 communities was only correlated with NH₄⁺-N at high nutrient loading (R² = 0.864, P = 0.001). Our results reveal the potential of using rrn copy number to evaluate the community sensitivity to nutrient disturbances, but community's historical contingency need to be taken in account.

Enhanced microbial metabolism in one stage partial nitritation-anammox system treating low strength wastewater by novel composite carrier

One stage partial nitritation-anammox (PN-A) process has attracted more and more attention due to the low investment cost but the instability in treating low strength wastewater. In this study, for producing a novel composite carrier that could provide high ammonia microenvironment in low strength wastewater, the zeolites and floating materials were combined in the spherical shell and distributed evenly by the spherical polyhedron. And a moving bed biofilm reactor (MBBR) with the composite carriers and ordinary carriers without zeolites as control group was operated for nearly 120 days. The PN-A process were realized in 53 days, and the total nitrogen removal efficiency reached around 85% at influent ammonium concentration of 50 mg/L finally. Analysis of 16S rRNA gene sequencing revealed that the composite carriers showed significant promotion on the proliferation of ammonium oxidizing bacteria (AOB) and enrichment of anaerobic ammonium oxidizing bacteria (AnAOB), accounting for 19.14% and 41.65% on the surface, respectively. Moreover, the existence of relative higher abundance of ammonia on the composite carrier surface was validated by the metabolite biomarker of glutamate and especially spermidine. The metabolomics analysis and 16S rRNA function prediction showed that the protein synthesis pathway was obviously upregulated on the composite carriers surface compared with that on the ordinary carriers surface. The higher abundance of glutamate and putrescine indicated that the composite carrier could stimulate the metabolism and growth of bacteria. The present study provided a functional carrier to realize the transformation of activated sludge system into PN-A system treating low strength wastewater, which is significant to the application of the process in mainstream.

Biodegradation of mixture of plastic films by tailored marine consortia

This work sheds light on the physicochemical changes of naturally weathered polymer surfaces along with changes of polymer buoyancy due to biofilm formation and degradation processes. To support the degradation hypothesis, a microcosm experiment was conducted where a mixture of naturally weathered plastic pieces was incubated with an indigenous pelagic community. A series of analyses were employed in order to describe the alteration of the physicochemical characteristics of the polymer (FTIR, SEC and GPC, sinking velocity) as well as the biofilm community (NGS). At the end of phase II, the fraction of double bonds in the surface of microbially treated PE films increased while changes were also observed in the profile of the PS films. The molecular weight of PE pieces increased with incubation time reaching the molecular weight of the virgin pieces (230,000 g mol^-1) at month 5 but the buoyancy displayed no difference throughout the experimental period. The number-average molecular weight of PS pieces decreased (33% and 27% in INDG and BIOG treatment respectively), implying chain scission; accelerated (by more than 30%) sinking velocities compared to the initial weathered pieces were also measured for PS films with biofilm on their surface. The orders Rhodobacterales, Oceanospirillales and Burkholderiales dominated the distinct platisphere communities and the genera Bacillus and Pseudonocardia discriminate these assemblages from the planktonic counterpart. The functional analysis predicts overrepresentation of adhesive cells carrying xenobiotic and hydrocarbon degradation genes. Taking these into account, we can suggest that tailored marine consortia have the ability to thrive in the presence of mixtures of plastics and participate in their degradation.

The genetic basis for adaptation of model-designed syntrophic co-cultures

Understanding the fundamental characteristics of microbial communities could have far reaching implications for human health and applied biotechnology. Despite this, much is still unknown regarding the genetic basis and evolutionary strategies underlying the formation of viable synthetic communities. By pairing auxotrophic mutants in co-culture, it has been demonstrated that viable nascent E. coli communities can be established where the mutant strains are metabolically coupled. A novel algorithm, OptAux, was constructed to design 61 unique multi-knockout E. coli auxotrophic strains that require significant metabolite uptake to grow. These predicted knockouts included a diverse set of novel non-specific auxotrophs that result from inhibition of major biosynthetic subsystems. Three OptAux predicted non-specific auxotrophic strains—with diverse metabolic deficiencies—were co-cultured with an L-histidine auxotroph and optimized via adaptive laboratory evolution (ALE). Time-course sequencing revealed the genetic changes employed by each strain to achieve higher community growth rates and provided insight into mechanisms for adapting to the syntrophic niche. A community model of metabolism and gene expression was utilized to predict the relative community composition and fundamental characteristics of the evolved communities. This work presents new insight into the genetic strategies underlying viable nascent community formation and a cutting-edge computational method to elucidate metabolic changes that empower the creation of cooperative communities.

Many basic characteristics underlying the establishment of cooperative growth in bacterial communities have not been studied in detail. The presented work sought to understand the adaptation of syntrophic communities by first employing a new computational method to generate a comprehensive catalog of E. coli auxotrophic mutants. Many of the knockouts in the catalog had the predicted effect of disabling a major biosynthetic process. As a result, these strains were predicted to be capable of growing when supplemented with many different individual metabolites (i.e., a non-specific auxotroph), but the strains would require a high amount of metabolic cooperation to grow in community. Three such non-specific auxotroph mutants from this catalog were co-cultured with a proven auxotrophic partner in vivo and evolved via adaptive laboratory evolution. In order to successfully grow, each strain in co-culture had to evolve under a pressure to grow cooperatively in its new niche. The non-specific auxotrophs further had to adapt to significant homeostatic changes in cell’s metabolic state caused by knockouts in metabolic genes. The genomes of the successfully growing communities were sequenced, thus providing unique insights into the genetic changes accompanying the formation and optimization of the viable communities. A computational model was further developed to predict how finite protein availability, a fundamental constraint on cell metabolism, could impact the composition of the community (i.e., the relative abundances of each community member).

Interactions in self-assembled microbial communities saturate with diversity

How the diversity of organisms competing for or sharing resources influences community function is an important question in ecology but has rarely been explored in natural microbial communities. These generally contain large numbers of species making it difficult to disentangle how the effects of different interactions scale with diversity. Here, we show that changing diversity affects measures of community function in relatively simple communities but that increasing richness beyond a threshold has little detectable effect. We generated self-assembled communities with a wide range of diversity by growth of cells from serially diluted seawater on brown algal leachate. We subsequently isolated the most abundant taxa from these communities via dilution-to-extinction in order to compare productivity functions of the entire community to those of individual taxa. To parse the effect of different types of organismal interactions, we defined relative total function (RTF) as an index for positive or negative effects of diversity on community function. Our analysis identified three overall regimes with increasing diversity. At low richness (<12 taxa), positive and negative effects of interactions were both weak, while at moderate richness (12–26 taxa), community resource uptake increased but the carbon use efficiency decreased. Finally, beyond 26 taxa, the effect of interactions on community function saturated and further diversity increases did not affect community function. Although more diverse communities had overall greater access to resources, on average individual taxa within these communities had lower resource availability and reduced carbon use efficiency. Our results thus suggest competition and complementation simultaneously increase with diversity but both saturate at a threshold.

A metabolomic view of how low nitrogen strength favors anammox biomass yield and nitrogen removal capability

The low yield of anaerobic ammonium oxidation (anammox) biomass has attracted great attention because of its difficulty to be abundantly enriched. Patterns of substrate supply greatly influence microbial metabolism and behavior. The present study proposed that low nitrogen strength was beneficial to anammox biomass yield and nitrogen removal when comparing a membrane bioreactor (MBR) operated at low nitrogen strength with short hydraulic retention time (HRT) (R-low; influent: fixed at 100 mg-N L^-1) and one operated at high nitrogen strength with long HRT (R-stepwise; influent: 100-700 mg-N L^-1). Different nitrite concentrations in the two MBRs would indicate discrepant environments, and inevitably resulted in the discrepant microbial responses for anammox community. In particular, we found that at low nitrogen strength, increased activities of purine and pyrimidine metabolism pathways provided more abundant nucleic acids for bacterial proliferation. More active reaction of lipid and protein synthesis favored the synthesis of cellular structure. Importantly, the metabolism of cheaper amino acids was more active under low nitrogen strength, which was coupled with higher metabolic flux and potentially more active exchange of costly amino acids as public goods. In this way, more energy could be saved and applied to biomass yield. Higher active bacterial diversity and more positive interactions among bacterial species in R-low further favored biomass yield and nitrogen removal. The present study highlighted the significant effect of substrate supply patterns on anammox, which is meaningful to overcome the current bottleneck of deficient anammox biomass for application in wastewater treatment.

Metabolic engineering of carbon overflow metabolism of Bacillus subtilis for improved N-acetyl-glucosamine production

Bacillus subtilis is widely used as cell factories for the production of important industrial biochemicals. Although many studies have demonstrated the effects of organic acidic byproducts, such as acetate, on microbial fermentation, little is known about the effects of blocking the neutral byproduct overflow, such as acetoin, on bioproduction. In this study, we focused on the influences of modulating overflow metabolism on the production of N-acetyl-d-glucosamine (GlcNAc) in engineered B. subtilis. We found that acetoin overflow competes with GlcNAc production, and blocking acetoin overflow increased GlcNAc titer and yield by 1.38- and 1.39-fold, reaching 48.9 g/L and 0.32 g GlcNAc/g glucose, respectively. Further blocking acetate overflow inhibited cell growth and GlcNAc production may be induced by inhibiting glucose uptake. Taken together, our results show that blocking acetoin overflow is a promising strategy for enhancing GlcNAc production. The strategies developed in this work may be useful for engineering strains of B. subtilis for producing other important biochemicals.

Environmental Factors Support the Formation of Specific Bacterial Assemblages on Microplastics

While the global distribution of microplastics (MP) in the marine environment is currently being critically evaluated, the potential role of MP as a vector for distinct microbial assemblages or even pathogenic bacteria is hardly understood. To gain a deeper understanding, we investigated how different in situ conditions contribute to the composition and specificity of MP-associated bacterial communities in relation to communities on natural particles. Polystyrene (PS), polyethylene (PE), and wooden pellets were incubated for 2 weeks along an environmental gradient, ranging from marine (coastal Baltic Sea) to freshwater (waste water treatment plant, WWTP) conditions. The associated assemblages as well as the water communities were investigated applying high-throughput 16S rRNA gene sequencing. Our setup allowed for the first time to determine MP-dependent and -independent assemblage factors as subject to different environmental conditions in one system. Most importantly, plastic-specific assemblages were found to develop solely under certain conditions, such as lower nutrient concentration and higher salinity, while the bacterial genus Erythrobacter, known for the ability to utilize polycyclic aromatic hydrocarbons (PAH), was found specifically on MP across a broader section of the gradient. We discovered no enrichment of potential pathogens on PE or PS; however, the abundant colonization of MP in a WWTP by certain bacteria commonly associated with antibiotic resistance suggests MP as a possible hotspot for horizontal gene transfer. Taken together, our study clarifies that the surrounding environment prevailingly shapes the biofilm communities, but that MP-specific assemblage factors exist. These findings point to the ecological significance of specific MP-promoted bacterial populations in aquatic environments and particularly in plastic accumulation zones.

On the intrinsic constraint of bacterial growth rate: M. tuberculosis's view of the protein translation capacity

In nature, the maximal growth rates vary widely among different bacteria species. Fast-growing bacteria species such as Escherichia coli can have a shortest generation time of 20 min. Slow-growing bacteria species are perhaps best known for Mycobacterium tuberculosis, a human pathogen with a generation time being no less than 16 h. Despite of the significant progress made on understanding the pathogenesis of M. tuberculosis, we know little on the origin of its intriguingly slow growth. From a global view, the intrinsic constraint of the maximal growth rate of bacteria remains to be a fundamental question in microbiology. In this review, we analyze and discuss this issue from the angle of protein translation capacity, which is the major demand for cell growth. Based on quantitative analysis, we propose four parameters: rRNA chain elongation rate, abundance of RNA polymerase engaged in rRNA synthesis, polypeptide chain elongation rate, and active ribosome fraction, which potentially limit the maximal growth rate of bacteria. We further discuss the relation of these parameters with the growth rate for M. tuberculosis as well as other bacterial species. We highlight future comprehensive investigation of these parameters for different bacteria species to understand how bacteria set their own specific growth rates.

Ecological strategies and metabolic trade-offs of complex environmental biofilms

Microorganisms aggregated into matrix-enclosed biofilms dominate microbial life in most natural, engineered, and medical systems. Despite this, the ecological adaptations and metabolic trade-offs of the formation of complex biofilms are currently poorly understood. Here, exploring the dynamics of bacterial ribosomal RNA operon (rrn) copy numbers, we unravel the genomic underpinning of the formation and success of stream biofilms that contain hundreds of bacterial taxa. Experimenting with stream biofilms, we found that nascent biofilms in eutrophic systems had reduced lag phases and higher growth rates, and more taxa with higher rrn copy number than biofilms from oligotrophic systems. Based on these growth-related traits, our findings suggest that biofilm succession was dominated by slow-but-efficient bacteria likely with leaky functions, such as the production of extracellular polymeric substances at the cost of rapid growth. Expanding our experimental findings to biofilms from 140 streams, we found that rrn copy number distribution reflects functional trait allocation and ecological strategies of biofilms to be able to thrive in fluctuating environments. These findings suggest that alternative trade-offs dominating over rate-yield trade-offs contribute to the evolutionary success of stream biofilms.

Analyzing natural biofilms containing many types of bacteria yields insights into microbial strategies for success in complex biofilms. The ecological adaptations and metabolic trade-offs involved in the formation of multi-bacterial biofilms in the environment are not well understood. Researchers in Switzerland and Austria, led by Tom Battin and Hannes Peter at the École Polytechnique Fédérale de Lausanne, performed genetic analysis of biofilms sampled from 140 streams. The biofilms contained hundreds of types of bacteria, unlike the mono-bacterial biofilms examined in many laboratory studies. Genetic analysis techniques revealed a diversity of metabolic strategies that allow bacteria to survive within the rich ecology of natural biofilms. Slow-growing but metabolically efficient bacteria that release more extracellular biofilm components thrive better than those adapted for quick growth alone. The findings significantly improve understanding of biofilm ecology in the natural environment.

Natural resource landscapes of a marine bacterium reveal distinct fitness-determining genes across the genome

Heterotrophic bacteria exploit diverse microhabitats in the ocean, from particles to transient gradients. Yet the degree to which genes and pathways can contribute to an organism's fitness on such complex and variable natural resource landscapes remains poorly understood. Here, we determine the gene-by-gene fitness of a generalist saprophytic marine bacterium (Vibrio sp. F13 9CS106) on complex resources derived from its natural habitats - copepods (Apocyclops royi) and brown algae (Fucus vesiculosus) - and as reference substrates, glucose and the polysaccharide alginate, derived from brown algal cell walls. We find that resource complexity strongly buffers fitness costs of mutations, and that anabolic rather than catabolic pathways are more stringently required, likely due to functional redundancy in the latter. Moreover, while carbohydrate-rich algae requires several synthesis pathways, protein-rich Apocyclops does not, suggesting this ancestral habitat for Vibrios is a replete medium with metabolically redundant substrates. We also identify a candidate fitness trade-off for algal colonization: deletion of mshA increases mutant fitness. Our results demonstrate that gene fitness depends on habitat composition, and suggest that this generalist uses distinct resources in different natural habitats. The results further indicate that substrate replete conditions may lead to relatively relaxed selection on catabolic genes.