Ecological strategies shape the insurance potential of biodiversity

Distinct co-succession of dissolved organic matter and bacterial generalists and specialists in inflow rivers of Baiyangdian Lake

Dissolved organic matter (DOM) significantly affects the stability of river microorganisms, but the seasonal regulatory mechanisms of generalists and specialists remain unclear. Through spectral measurement and high-throughput sequencing techniques, the structural, network, and evolutionary characteristics of generalists and specialists in Baiyangdian lake inflow rivers from 2021 to 2023 were analyzed, and the influences of environmental factors and DOM on their dynamics were quantified. Parallel factor analysis (PARAFAC) identified two protein-like components (C1+C2) and one humus-like component (C3). Among them, the protein-like components were significantly higher in urban reclaimed water (URW) than in non-urban reclaimed water (NRW), while the humus-like component was higher in summer than in winter (P < 0.001). The relative concentration of DOM was higher in summer, showing overall low humification and strong autochthonous characteristics (FI > 1.8, HIX <4). Actinobacteriota and Proteobacteria were the main components of generalists and specialists. Species replacement had a much greater impact on β-diversity than richness differences. The network structure of winter and NRW exhibited more complex topological properties, and the stability of generalist networks was lower than that of specialists. Stochastic processes dominated the community assembly process (63.73 %-93.94 %), with generalists in summer being more influenced by stochastic processes, while the opposite was true in winter. The BiSSE model indicated that specialists exhibited higher diversification potential than generalists. Path analysis showed that in summer URW, diversity and protein-like components had the greatest impact on the network stability of generalists and specialists, respectively. In NRW, humus-like component had the greatest impact on the network stability of specialists. This study clarified the mechanism by which the seasonal characteristics of DOM drive the ecological strategy differentiation of generalists and specialists in rivers, providing a theoretical basis for watershed ecological management.

Specialists regulate microbial network and community assembly in subtropical seagrass sediments under differing land use conditions

Microorganisms in the sediment play a pivotal role in the functioning and stability of seagrass ecosystems and their dynamics are influenced by the nutrient acquisition strategies of host plants. While the distinct impacts of microbial generalists and specialists on community dynamics are recognized, their distribution patterns and ecological roles within seagrass ecosystems remain largely unexplored. To address this issue, we conducted an analysis of community assembly processes and co-occurrence relationships of both microbial generalists and specialists within sediment profiles (0-100 cm) from seagrass habitats subjected to differing land use conditions. The results revealed that seagrasses in Yifeng Estuary experienced the large proportion of cultivated land and exhibited higher organic carbon content in the 0-20 cm surface sediment layer. Nitrogen-cycling bacteria were predominantly associated with seagrasses from Yifeng Estuary, whereas Vibrio spp. was more prevalent in seagrasses from Liusha Bay. Notably, seagrass Halophia beccarii (YHB) in Yifeng Estuary harbored higher niche breadths for both microbial generalist and specialist compared to Halodule uninervis (LHU) and Halophia ovalis (LHO) from Liusha Bay. Stochastic processes were pivotal in shaping seagrass sediment microbial communities, with a higher immigration rate observed in YHB, suggesting greater microbial turnover in this area. Additionally, YHB sediment presented lower drift and higher dispersal limitation among generalists compared to LHU and LHO, whereas the pattern was reversed among specialists. Specialists were found to play a crucial role in shaping microbial interactions within YHB sediment, with genera Halioglobus identified as keystone species in the network. The specialists were further found to significantly influence microbial β-diversity in seagrass sediment directly. Overall, our findings illustrated how microbial generalists and specialists were distributed in seagrass sediments in response to land use changes and provided new insights into the potential roles of microbial regulation in degraded seagrass ecosystems.

Microbiome analysis in Asia's largest watershed reveals inconsistent biogeographic pattern and microbial assembly mechanisms in river and lake systems

Microorganisms are critical to the stability of aquatic environments, and understanding the ecological mechanisms of microbial community is essential. However, the distinctions and linkages across biogeographic patterns, ecological processes, and formation mechanisms of microbes in rivers and lakes remain unknown. Accordingly, microbiome-centric analysis was conducted in rivers and lakes in the Yangtze River watershed. Results revealed significant differences in the structure and diversity of microbial communities between rivers and lakes, with rivers showing higher diversity. Lakes exhibited lower community stability, despite higher species interactions. Although deterministic processes dominated microbial community assembly both in rivers and lakes, higher stochastic processes of rare and abundant taxa exhibited in rivers. Spatial factors influenced river microbial community, while environmental factors drove differences in the lake bacterial community. This study deepened the understanding of microbial biogeography and formation mechanisms in large watershed rivers and lakes, highlighting distinct community aggregation patterns between river and lake microorganisms.

Plant diversity increases spatial stability of aboveground productivity in alpine grasslands

Plant diversity can significantly affect the grassland productivity and its stability. However, it remains unclear how plant diversity affects the spatial stability of natural grassland productivity, especially in alpine regions that are sensitive to climate change. We analyzed the interaction between plant (species richness and productivity, etc.) and climatic factors (precipitation, temperature, and moisture index, etc.) of alpine natural grassland on the Qinghai-Tibetan Plateau. In addition, we tested the relationship between plant diversity and spatial stability of grassland productivity. Results showed that an increase in plant diversity significantly enhanced community productivity and its standard deviation, while reducing the coefficient of variation in productivity. The influence of plant diversity on productivity and the reciprocal of productivity variability coefficient was not affected by vegetation types. The absolute values of the regression slopes between climate factors and productivity in alpine meadow communities with higher plant diversity were smaller than those in alpine meadow communities with lower plant diversity. In other words, alpine meadow communities with higher plant diversity exhibited a weaker response to climatic factors in terms of productivity, whereas those with lower plant diversity showed a stronger response. Our results indicate that high plant diversity buffers the impact of ambient pressure (e.g., precipitation, temperature) on alpine meadow productivity, and significantly enhanced the spatial stability of grassland productivity. This finding provides a theoretical basis for maintaining the stability of grassland ecosystems and scientifically managing alpine grasslands under the continuous climate change.

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophication on bacterial communities from coastal ecosystems. The functional stability of these communities is critically important for maintaining water quality, productivity, and ecosystem services, such as fishery yields. Microbial functional stability can be maintained via resistance and resilience, which are reflected in genomic traits such as genome size and codon usage bias and may be linked to metabolic costs. However, little is known about the mechanisms that select these traits under varying nutrient regimes. To study the impact of pulsed disturbances on community assembly and functioning depending on metabolic costs, we performed a 41-day pulse disturbance experiment across two levels of resource availability. Our setup triggered stochastic community re-assembly processes in all treatments. In contrast, we observed consistent and resource availability-dependent patterns of superordinate community functioning and structural patterns, such as functional resistance in response to disturbances, genomic trait distributions, and species diversity. Predicted genomic traits reflected the selection for taxa possessing resistant- and resilience-related traits, particularly under high nutrient availability. Our findings are a step toward unraveling the compositional and genomic underpinnings of functional resistance in microbial communities after exposure to consecutive pulse disturbances. Our work demonstrates how resource availability alleviates metabolic constraints on resistance and resilience, and this has important consequences for predicting water quality and ecosystem productivity of environments exposed to global change.

IMPORTANCE

Understanding the communities' responses to disturbances is a prerequisite to predicting ecosystem dynamics and, thus, highly relevant considering global change. Microbial communities play key roles in numerous ecosystem functions and services, and the large diversity, rapid growth, and phenotypic plasticity of microorganisms are thought to allow high resistance and resilience. While potential metabolic costs associated with adaptations to fluctuating environments have been debated, little evidence supports trade-offs between resource availability, resistance, and resilience. Here, we experimentally assessed the compositional and functional responses of an aquatic microbial model community to disturbances and systematically manipulated resource availability. Our results demonstrate that the capacity to tolerate environmental fluctuations is constrained by resource availability and reflected in the selection of genomic traits.

Characterizing the microbiome of patients with myeloproliferative neoplasms during a Mediterranean diet intervention

IMPORTANCE

The gut microbiome serves as an interface between the host and the diet. Diet and the gut microbiome both play important roles in managing inflammation, which is a key aspect of myeloproliferative neoplasm (MPN). Studies have shown that a Mediterranean (MED) diet can reduce inflammation. Therefore, we longitudinally characterized the gut microbiomes of MPN patients in response to Mediterranean or standard 2020 US Guidelines for Americans dietary counseling to determine whether there were microbiome-associated changes in inflammation. We did not find significant changes in the gut microbiome associated with diet, but we did find several associations with inflammation. This research paves the way for future studies by identifying potential mechanistic targets implicated in inflammation within the MPN gut microbiome.

Irreversible community difference between bacterioplankton generalists and specialists in response to lake dredging

Understanding response of bacterioplankton community responsible for maintaining ecological functions of aquatic ecosystems to environmental disturbance is an important subject. However, it remains largely unclear how bacterioplankton generalists and specialists respond to dredging disturbance. Illumina MiSeq sequencing and statistical analyses were used to evaluate landscape patterns, evolutionary potentials, environmental adaptability, and community assembly processes of generalists and specialists in response to dredging in eutrophic Lake Nanhu. The Proteobacteria and Actinobacteria dominated bacterioplankton communities of generalists and specialists, and abundances of Proteobacteria decreased and Actinobacteria increased after dredging. The generalists displayed higher phylogenetic distance, richness difference, speciation rate, extinction rate, and diversification rate as well as stronger environmental adaptation than that of specialists. In contrast, the specialists rather than generalists showed higher community diversity, taxonomic distance, and species replacement as well as closer phylogenetic clustering. Stochastic processes dominated community assemblies of generalists and specialists, and stochasticity exhibited a larger effect on community assembly of generalists rather than specialists. Our results emphasized that lake dredging could change landscape patterns of bacterioplankton generalists and specialists, whereas the short-term dredging conducted within one year was unable to reverse community difference between generalists and specialists. Our findings extend our understanding of how bacterioplankton generalists and specialists responding to dredging disturbance, and these findings might in turn call on long-term dredging for better ecological restoration of eutrophic lakes.

Shifts in the bacterial community caused by combined pollutant loads in the North Canal River, China

A typical anthropogenically disturbed urban river polluted by a combination of conventional pollutants (nitrogen and phosphorus pollution) and heavy metals was investigated along a 238 km stretch. Changes in the bacterial community were evaluated using high-throughput sequencing, and the relationships between bacteria, heavy metals, and conventional pollutants were investigated. There was large spatial heterogeneity in the bacterial community along the river, and bacterial diversity in the upstream and midstream sections was much higher than in the downstream section. Heavy metals and conventional pollutants both exhibited close correlations with bacterial diversity and composition. For instance, potential fecal indicator bacteria, sewage indicator bacteria and pathogenic bacteria, such as Ruminococcus and Pseudomonas, were closely associated with Cu, Zn, and NH₄⁺-N. Rather than conventional pollutants, heavy metals were the main driving factors of the microbial community characteristics. These results confirm that bacterial communities play a crucial role in biogeochemical cycles. Therefore, heavy metals could be used as biomarkers of complex pollution to indicate the pollution status of riverine ecosystems and contribute to the restoration of habitats in anthropogenically disturbed urban rivers.

Water quality profits by the submerged macrophyte community consisting of multi-functional species-rich groups

The re-establishment of submerged macrophytes facilitates the formation of a clear-water state in shallow eutrophic lakes. But most restorations of submerged macrophytes are often unstable and cannot maintain a stable clear-water state, probably because the species and functional diversity have not been fully taken into account. In this study, we try to explore submerged macrophyte communities and water quality changes under different submerged macrophyte combinations through mesocosm experiments. We hypothesized that communities with high species and functional diversity would be more conducive to improving water quality. The results showed that the mean community biomass of single-species and 8-species were higher than 5-species. And the stability and mean relative growth rate of the 8-species community were higher than the 5-species community. With the same configuration of three functional groups, the 8-species community was more stable and had better water quality than the 5-species community. The path analysis revealed that different functional groups of submerged macrophytes play different roles. The erect and canopy-producing submerged macrophytes were conducive to reducing total suspended solids (TSS) concentrations in the water column during community construction. In contrast, bottom-dwelling submerged macrophytes were conducive to reducing total nitrogen, total phosphorus, and TSS concentrations during the stage of disturbances. Our results also suggested that canopy-producing groups may have a competitive advantage for light over bottom-dwelling species. Based on the above results and biodiversity insurance hypothesis, we conclude that the community consisting of multi-functional species-rich groups is conducive to building stable submerged macrophyte communities and obtaining a stable clear-water state. Our findings will improve water quality management and pollution control for eutrophic shallow lakes.

Distribution of sediment microbial communities and their relationship with surrounding environmental factors in a typical rural river, Southwest China

With rapid urbanization and industrialization, rural rivers in China are facing deterioration in water quality and ecosystem health. Microorganisms living in river sediments are involved in biogeochemical processes, mineralization, and degradation of pollutants. Understanding bacterial community distribution in rural rivers could help evaluate the response of river ecosystems to environmental pollution and understand the river self-purification mechanism. In this study, the relationship between characteristics of sediment microbial communities and the surrounding environmental factors in a typical rural river was analyzed using 16S rRNA gene sequencing technology. The results showed that the dominant bacterial groups in the river sediment were Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Firmicutes, accounting for 83.61% of the total microbial load. Different areas have different sources of pollution which give rise to specific dominant bacteria. The upstream part of the river flows through an agricultural cultivation area where the dominant bacteria were norank_f_Gemmatimonadaceae, Haliangium, and Pseudolabrys, possessing obvious nitrogen- and phosphorus-metabolizing activities. The midstream section flows through an urban area where the dominant bacteria were Marmoricola, Nocardioides, Gaiella, Sphingomonas, norank_f_67-14, Subgroup_10, Agromyces, and Lysobacter, with strong metabolizing activity for toxic pollutants. The dominant bacteria in the downstream part were Clostridium_sensu_stricto_1, norank_f__Bacteroidetes_vadinHA17, Candidatus_Competibacter, and Methylocystis. Redundancy analysis and correlation heatmap analysis showed that environmental factors: ammonia nitrogen (NH₄⁺-N) and total nitrogen (TN) in the sediment, and pH, temperature, TN, electrical conductivity (EC), and total dissolved solids (TDS) in the water, significantly affected the bacterial community in the sediment. The PICRUSt2 functional prediction analysis identified that the main function of bacteria in the sediment was metabolism (77.3%), specifically carbohydrate, amino acid, and energy metabolism. These activities are important for degrading organic matter and removing pollutants from the sediments. The study revealed the influence of organic pollutants derived from human activities on the bacterial community composition in the river sediments. It gave a new insight into the relationship between environmental factors and bacterial community distribution in rural watershed ecosystems, providing a theoretical basis for self-purification and bioremediation of rural rivers.

The hallmarks of dietary intervention-resilient gut microbiome

Maintaining equilibrium of the gut microbiome is crucial for human health. Diet represents an important and generally accessible natural channel of controlling the nutrients supply to the intestinal microorganisms. Although many studies showed that dietary interventions can specifically modulate gut microbiome composition, further progress of the approach is complicated by interindividual variability of the microbial community response. The reported causes of this variability include the baseline microbiome composition features, but it is unclear whether any of them are intervention-specific. Here, we applied a unified computational framework to investigate the variability of microbiome response measured as beta diversity in eight various dietary interventions using previously published 16S rRNA sequencing datasets. We revealed a number of baseline microbiome features which determine the microbiome response in an intervention-independent manner. One of the most stable associations, reproducible for different interventions and enterotypes, was a negative dependence of the response on the average number of genes per microorganism in the community—an indicator of the community functional redundancy. Meanwhile, many revealed microbiome response determinants were enterotype-specific. In Bact1 and Rum enterotypes, the response was negatively correlated with the baseline abundance of their main drivers. Additionally, we proposed a method for preliminary assessment of the microbiome response. Our study delineats the universal features determining microbiome response to diverse interventions. The proposed approach is promising for understanding the mechanisms of gut microbiome stability and improving the efficacy of personalised microbiome-tailored interventions.

Niche breadth affects bacterial transcription patterns along a salinity gradient

Understanding the molecular mechanisms that determine a species' life history is important for predicting their susceptibility to environmental change. While specialist species with a narrow niche breadth (NB) maximize their fitness in their optimum habitat, generalists with broad NB adapt to multiple environments. The main objective of this study was to identify general transcriptional patterns that would distinguish bacterial strains characterized by contrasted NBs along a salinity gradient. More specifically, we hypothesized that genes encoding fitness-related traits, such as biomass production, have a higher degree of transcriptional regulation in specialists than in generalists, because the fitness of specialists is more variable under environmental change. By contrast, we expected that generalists would exhibit enhanced transcriptional regulation of genes encoding traits that protect them against cellular damage. To test these hypotheses, we assessed the transcriptional regulation of fitness-related and adaptation-related genes of 11 bacterial strains in relation to their NB and stress exposure under changing salinity conditions. The results suggested that transcriptional regulation levels of fitness- and adaptation-related genes correlated with the NB and/or the stress exposure of the inspected strains. We further identified a shortlist of candidate stress marker genes that could be used in future studies to monitor the susceptibility of bacterial populations or communities to environmental changes.

Many roads to bacterial generalism

The fundamental niches of bacteria can be defined along many environmental axes, including temperature tolerance and resources consumed, while interactions with other organisms can constrain (e.g. competition) or enlarge (e.g. cross-feeding) realized niches. Organisms are often categorized as generalists or specialists, corresponding to broad or narrow niche requirements, which can then be linked to their functional role in an ecosystem. We show how these terms are applied to bacteria, make predictions about how the type and extent of generalism displayed by an organism relates to its functional potential and discuss the value of collecting different types of generalist bacteria. We believe that new approaches that take advantage of both high-throughput sequencing and environmental manipulation can allow us to understand the many types of generalism found within both cultivated and yet-to-be-cultivated bacteria.

Cryopreservation and Resuscitation of Natural Aquatic Prokaryotic Communities

Experimental reproducibility in aquatic microbial ecology is critical to predict the dynamics of microbial communities. However, controlling the initial composition of naturally occurring microbial communities that will be used as the inoculum in experimental setups is challenging, because a proper method for the preservation of those communities is lacking. To provide a feasible method for preservation and resuscitation of natural aquatic prokaryote assemblages, we developed a cryopreservation procedure applied to natural aquatic prokaryotic communities. We studied the impact of inoculum size, processing time, and storage time on the success of resuscitation. We further assessed the effect of different growth media supplemented with dissolved organic matter (DOM) prepared from naturally occurring microorganisms on the recovery of the initially cryopreserved communities obtained from two sites that have contrasting trophic status and environmental heterogeneity. Our results demonstrated that the variability of the resuscitation process among replicates decreased with increasing inoculum size. The degree of similarity between initial and resuscitated communities was influenced by both the growth medium and origin of the community. We further demonstrated that depending on the inoculum source, 45-72% of the abundant species in the initially natural microbial communities could be detected as viable cells after cryopreservation. Processing time and long-term storage up to 12 months did not significantly influence the community composition after resuscitation. However, based on our results, we recommend keeping handling time to a minimum and ensure identical incubation conditions for repeated resuscitations from cryo-preserved aliquots at different time points. Given our results, we recommend cryopreservation as a promising tool to advance experimental research in the field of microbial ecology.

Changes in Microbial Community Structures under Reclaimed Water Replenishment Conditions

Using reclaimed water as a resource for landscape water replenishment may alleviate the major problems of water resource shortages and water environment pollution. However, the safety of the reclaimed water and the risk of eutrophication caused by the reclaimed water replenishment are unclear to the public and to the research community. This study aimed to reveal the differences between natural water and reclaimed water and to discuss the rationality of reclaimed water replenishment from the perspective of microorganisms. The microbial community structures in natural water, reclaimed water and natural biofilms were analyzed, and the community succession was clarified along the ecological niches, water resources, fluidity and time using 16S rRNA gene amplicon sequencing. Primary biofilms without the original community were added to study the formation of microbial community structures under reclaimed water acclimation. The results showed that the difference caused by ecological niches was more than those caused by the fluidity of water and different water resources. No significant difference caused by the addition of reclaimed water was found in the microbial diversity and community structure. Based on the results of microbial analysis, reclaimed water replenishment is a feasible solution that can be used for supplying river water.

Higher contribution of globally rare bacterial taxa reflects environmental transitions across the surface ocean

Microbial taxa range from being ubiquitous and abundant across space to extremely rare and endemic, depending on their ecophysiology and on different processes acting locally or regionally. However, little is known about how cosmopolitan or rare taxa combine to constitute communities and whether environmental variations promote changes in their relative abundances. Here we identified the Spatial Abundance Distribution (SpAD) of individual prokaryotic taxa (16S rDNA-defined Operational Taxonomic Units, OTUs) across 108 globally-distributed surface ocean stations. We grouped taxa based on their SpAD shape ("normal-like"- abundant and ubiquitous; "logistic"- globally rare, present in few sites; and "bimodal"- abundant only in certain oceanic regions), and investigated how the abundance of these three categories relates to environmental gradients. Most surface assemblages were numerically dominated by a few cosmopolitan "normal-like" OTUs, yet there was a gradual shift towards assemblages dominated by "logistic" taxa in specific areas with productivity and temperature differing the most from the average conditions in the sampled stations. When we performed the SpAD categorization including additional habitats (deeper layers and particles of varying sizes), the SpAD of many OTUs changed towards fewer "normal-like" shapes, and OTUs categorized as globally rare in the surface ocean became abundant. This suggests that understanding the mechanisms behind microbial rarity and dominance requires expanding the context of study beyond local communities and single habitats. We show that marine bacterial communities comprise taxa displaying a continuum of SpADs, and that variations in their abundances can be linked to habitat transitions or barriers that delimit the distribution of community members.

A low proportion of rare bacterial taxa responds to abiotic changes compared with dominant taxa

In many studies, rare bacterial taxa have been found to increase in response to environmental changes. These changes have been proposed to contribute to the insurance of ecosystem functions. However, it has not been systematically tested if rare taxa are more likely to increase in abundance than dominant taxa. Here, we study whether rare soil bacterial taxa are more likely to respond to environmental disturbances and if rare taxa are more opportunistic than dominant taxa. To test this, we applied nine different disturbance treatments to a grassland soil and observed changes in bacterial community composition over 7 days. While 12% of the dominant taxa changed in abundance, only 1% of the rare taxa showed any effect. Rare taxa increased in response to a single disturbance treatment only, while dominant taxa responded to up to five treatments. We conclude that rare taxa are not more likely to contribute to community dynamics after disturbances than dominant taxa. Nevertheless, as rare taxa outnumber abundant taxa with here 230 taxa that changed significantly, the chance is high that some of these rare taxa might act as ecologically important keystone taxa. Therefore, rare and abundant taxa might both contribute to ecosystem insurance.

Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85-90 °N

Larger volumes of sea ice have been thawing in the Central Arctic Ocean (CAO) during the last decades than during the past 800,000 years. Brackish brine (fed by meltwater inside the ice) is an expanding sympagic habitat in summer all over the CAO. We report for the first time the structure of bacterial communities in this brine. They are composed of psychrophilic extremophiles, many of them related to phylotypes known from Arctic and Antarctic regions. Community structure displayed strong habitat segregation between brackish ice brine (IB; salinity 2.4-9.6) and immediate sub-ice seawater (SW; salinity 33.3-34.9), expressed at all taxonomic levels (class to genus), by dominant phylotypes as well as by the rare biosphere, and with specialists dominating IB and generalists SW. The dominant phylotypes in IB were related to Candidatus Aquiluna and Flavobacterium, those in SW to Balneatrix and ZD0405, and those shared between the habitats to Halomonas, Polaribacter and Shewanella. A meta-analysis for the oligotrophic CAO showed a pattern with Flavobacteriia dominating in melt ponds, Flavobacteriia and Gammaproteobacteria in solid ice cores, Flavobacteriia, Gamma- and Betaproteobacteria, and Actinobacteria in brine, and Alphaproteobacteria in SW. Based on our results, we expect that the roles of Actinobacteria and Betaproteobacteria in the CAO will increase with global warming owing to the increased production of meltwater in summer. IB contained three times more phylotypes than SW and may act as an insurance reservoir for bacterial diversity that can act as a recruitment base when environmental conditions change.

Adaptive shifts of bacterioplankton communities in response to nitrogen enrichment in a highly polluted river

Anthropogenic activity-mediated nutrient pollution, especially nitrogen enrichment, poses one of the major threats to river ecosystems. However, it remains unclear how and to which extent it affects aquatic microbial communities, especially in heavily polluted rivers. In this study, a significant environmental gradient, particularly nitrogen gradient, was observed along a wastewater receiving river, the North Canal River (NCR). The pollution level was highest, moderate, and lowest in the up-, middle, and down-streams, respectively. The community composition of bacterioplankton transitioned from being Betaproteobacteria-dominated upstream to Gammaproteobacteria-dominated downstream. Copiotrophic groups, such as Polynucleobacter (Betaproteobacteria) and Hydrogenophaga (Betaproteobacteria), were dominant in the upstream. Multiple statistical analyses indicated that total nitrogen (TN) was the most important factor driving the adaptive shifts of community structure. Analyses of co-occurrence networks showed that the complexity of networks was disrupted in the up- and middle streams, while enhanced in the downstream. Our findings here suggested that microbial interactions were reduced in response to the aggravation of nutrient pollution. Similar to these changes, we observed significant dissimilarity of composition of functional groups, with highest abundance of nitrogen metabolism members under the highest level of nitrogen enrichment. Further analyses indicated that most of these functional groups belonged to Betaproteobacteria, suggesting the potential coupling of community composition and function diversity. In summary, adaptive shifts of bacterioplankton community composition, as well as species interactions, occurred in response to nutrient pollution in highly polluted water bodies.

Reevaluating the Salty Divide: Phylogenetic Specificity of Transitions between Marine and Freshwater Systems

Marine and freshwater microbial communities are phylogenetically distinct, and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing data sets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages. At the same time, and contrary to expectations, many shared taxa were observed in both habitats. Based on several metrics, we found that Gammaproteobacteria, Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria contained the highest number of closely related marine and freshwater sequences, suggesting comparatively recent habitat transitions in these groups. Using the abundant alphaproteobacterial group SAR11 as an example, we found evidence that new lineages, beyond the recognized LD12 clade, are detected in freshwater at low but reproducible abundances; this evidence extends beyond the 16S rRNA locus to core genes throughout the genome. Our results suggest that shared taxa are numerous, but tend to occur sporadically and at low relative abundance in one habitat type, leading to an underestimation of transition frequency between marine and freshwater habitats. Rare taxa with abundances near or below detection, including lineages that appear to have crossed the salty divide relatively recently, may possess adaptations enabling them to exploit opportunities for niche expansion when environments are disturbed or conditions change. IMPORTANCE The distribution of microbial diversity across environments yields insight into processes that create and maintain this diversity as well as potential to infer how communities will respond to future environmental changes. We integrated data sets from dozens of freshwater lake and marine samples to compare diversity across open water habitats differing in salinity. Our novel combination of sequence-based approaches revealed lineages that likely experienced a recent transition across habitat types. These taxa are promising targets for studying physiological constraints on salinity tolerance. Our findings contribute to understanding the ecological and evolutionary controls on microbial distributions, and open up new questions regarding the plasticity and adaptability of particular lineages.

Competition and niche separation of pelagic bacteria in freshwater habitats

Freshwater bacterioplankton assemblages are composed of sympatric populations that can be delineated, for example, by ribosomal RNA gene relatedness and that differ in key ecophysiological properties. They may be free-living or attached, specialized for particular concentrations or subsets of substrates, or invest a variable amount of their resources in defence traits against protistan predators and viruses. Some may be motile and tactic whereas others are not, with far-reaching implications for their respective life styles and niche partitioning. The co-occurrence of competitors with overlapping growth requirements has profound consequences for the stability of community functions; it can to some extent be explained by habitat factors such as the microscale complexity and spatiotemporal variability of the lacustrine environments. On the other hand, the composition and diversity of freshwater microbial assemblages also reflects non-equilibrium states, dispersal and the stochasticity of community assembly processes. This review synoptically discusses the competition and niche separation of heterotrophic bacterial populations (defined at various levels of phylogenetic resolution) in the pelagic zone of inland surface waters from a variety of angles, focusing on habitat heterogeneity and the resulting biogeographic distribution patterns, the ecophysiological adaptations to the substrate field and the interactions of prokaryotes with predators and viruses.

Initial nitrogen enrichment conditions determines variations in nitrogen substrate utilization by heterotrophic bacterial isolates

Background

The nitrogen (N) cycle consists of complex microbe-mediated transformations driven by a variety of factors, including diversity and concentrations of N compounds. In this study, we examined taxonomic diversity and N substrate utilization by heterotrophic bacteria isolated from streams under complex and simple N-enrichment conditions.

Results

Diversity estimates differed among isolates from the enrichments, but no significant composition were detected. Substrate utilization and substrate range of bacterial assemblages differed within and among enrichments types, and not simply between simple and complex N-enrichments.

Conclusions

N substrate use patterns differed between isolates from some complex and simple N-enrichments while others were unexpectedly similar. Taxonomic composition of isolates did not differ among enrichments and was unrelated to N use suggesting strong functional redundancy. Ultimately, our results imply that the available N pool influences physiology and selects for bacteria with various abilities that are unrelated to their taxonomic affiliation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-017-0993-7) contains supplementary material, which is available to authorized users.

Predicting biotic interactions and their variability in a changing environment

Global environmental change is altering the patterns of biodiversity worldwide. Observation and theory suggest that species' distributions and abundances depend on a suite of processes, notably abiotic filtering and biotic interactions, both of which are constrained by species' phylogenetic history. Models predicting species distribution have historically mostly considered abiotic filtering and are only starting to integrate biotic interaction. However, using information on present interactions to forecast the future of biodiversity supposes that biotic interactions will not change when species are confronted with new environments. Using bacterial microcosms, we illustrate how biotic interactions can vary along an environmental gradient and how this variability can depend on the phylogenetic distance between interacting species.

Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms

Resources structure ecological communities and potentially link biodiversity to energy flow. It is commonly believed that functional traits (generalists versus specialists) involved in the exploitation of resources depend on resource availability and environmental fluctuations. The longitudinal nature of stream ecosystems provides changing resources to stream biota with yet unknown effects on microbial functional traits and community structure. We investigated the impact of autochthonous (algal extract) and allochthonous (spruce extract) resources, as they change along alpine streams from above to below the treeline, on microbial diversity, community composition and functions of benthic biofilms. Combining bromodeoxyuridine labelling and 454 pyrosequencing, we showed that diversity was lower upstream than downstream of the treeline and that community composition changed along the altitudinal gradient. We also found that, especially for allochthonous resources, specialisation by biofilm bacteria increased along that same gradient. Our results suggest that in streams below the treeline biofilm diversity, specialisation and functioning are associated with increasing niche differentiation as potentially modulated by divers allochthonous and autochthonous constituents contributing to resources. These findings expand our current understanding on biofilm structure and function in alpine streams.

Deciphering microbial community robustness through synthetic ecology and molecular systems synecology

Microbial ecosystems exhibit specific robustness attributes arising from the assembly and interaction networks of diverse, heterogeneous communities challenged by fluctuating environmental conditions. Synthetic ecology provides new insights into key biodiversity-stability relationships and robustness determinants of host-associated or environmental microbiomes. Driven by the advances of meta-omics technologies and bioinformatics, community-centered approaches (defined as molecular systems synecology) combined with the development of dynamic and mechanistic mathematical models make it possible to decipher and predict the outcomes of microbial ecosystems under disturbances. Beyond discriminating the normal operating range and natural, intrinsic dynamics of microbial processes from systems-level responses to environmental forcing, predictive modeling is poised to be integrated within prescriptive analytical frameworks and thus provide guidance in decision-making and proactive microbial resource management.