Taxonomic variability and functional stability in microbial communities infected by phages

Mass-immigration shapes the antibiotic resistome of wastewater treatment plants

Wastewater treatment plants (WWTPs) are the hotspots for the spread of antibiotic resistance genes (ARGs) into the environment. Nevertheless, a comprehensive assessment of the city-level and short-term daily (inter-day) variations of ARG profiles in the whole process (influent-INF, activated sludge-AS and effluent-EF) of WWTPs is still lacking. Here, 285 ARGs and ten mobile gene elements were monitored in seven WWTPs in Xiamen for seven days via high-throughput qPCR. The average daily load of ARGs to WWTPs was about 1.32 × 1020 copies/d, and a total of 1.56 × 1018 copies/d was discharged to the environment across the entire city. Stochastic processes were the main force determining the assembly of ARG communities during sampling campaign, with their relative importance ranked in the order of INF > EFF > AS. There're little daily variations in ARG richness, abundance, β-diversity composition as well as assembly mechanisms. The results of SourceTracker, variation partitioning analysis, and hierarchical partitioning analysis indicated that bacteria and ARGs from upstream treatment processes played an increasingly dominant role in shaping ARG communities in AS and EFF, respectively, suggesting the importance of mass-immigration of bacteria and ARGs from the source on ARG transport in wastewater treatment processes. This emphasizes the need to revise the way we mitigate ARG contamination but focus on the source of ARGs in urban wastewater.

Searching for Principles of Microbial Ecology Across Levels of Biological Organization

Microbial communities play pivotal roles in ecosystems across different scales, from global elemental cycles to household food fermentations. These complex assemblies comprise hundreds or thousands of microbial species whose abundances vary over time and space. Unraveling the principles that guide their dynamics at different levels of biological organization, from individual species, their interactions, to complex microbial communities, is a major challenge. To what extent are these different levels of organization governed by separate principles, and how can we connect these levels to develop predictive models for the dynamics and function of microbial communities? Here, we will discuss recent advances that point towards principles of microbial communities, rooted in various disciplines from physics, biochemistry, and dynamical systems. By considering the marine carbon cycle as a concrete example, we demonstrate how the integration of levels of biological organization can offer deeper insights into the impact of increasing temperatures, such as those associated with climate change, on ecosystem-scale processes. We argue that by focusing on principles that transcend specific microbiomes, we can pave the way for a comprehensive understanding of microbial community dynamics and the development of predictive models for diverse ecosystems.

Viral diversity and dynamics and CRISPR-Cas-mediated immunity in a robust alkaliphilic cyanobacterial consortium

IMPORTANCE

Biotechnology applications utilizing the function of microbial communities have become increasingly important solutions as we strive for sustainable applications. Although viral infections are known to have a significant impact on microbial turnover and nutrient cycling, viral dynamics have remained largely overlooked in these engineered communities. Predatory perturbations to the functional stability of these microbial biotechnology applications must be investigated in order to design more robust applications. In this study, we closely examine virus-microbe dynamics in a model microbial community used in a biotechnology application. Our findings suggest that viral dynamics change significantly with environmental conditions and that microbial immunity may play an important role in maintaining functional stability. We present this study as a comprehensive template for other researchers interested in exploring predatory dynamics in engineered microbial communities.

Narrow host range phages infect essential bacteria for water purification reactions in groundwater-fed rapid sand filters

Biofiltration is used worldwide to provide safe potable water due to its low energy demand and excellent treatment performance. For instance, in Denmark, over 95% of drinking water is supplied through groundwater-fed rapid sand filters (RSF). Bacteriophages, viruses that infect bacteria, have been shown to shape the taxonomic and functional composition of microbial communities across a range of natural and engineering systems. However, phages in the biofiltration systems are rarely studied, despite the central role microbes play in water purification. To probe this, metagenomic data from surface water, groundwater and mixed source water biofiltration units (n = 26 from China, Europe and USA) for drinking water production were analysed to characterize prokaryotic viruses and to identify their potential microbial hosts. The source water type and geographical location are found to exert influence on the composition of the phageome in biofilters. Although the viral abundance (71,676 ± 17,841 RPKM) in biofilters is only 14.4% and 17.0% lower than those of the nutrient-rich wastewater treatment plants and fresh surface waters, the richness (1,441 ± 1,046) and diversity (Inverse Simpson: 91 ± 61) in biofiltration units are significantly less by a factor of 2-5 and 3-4, respectively. In depth analysis of data from 24 groundwater-fed RSFs in Denmark revealed a core phageome shared by most RSFs, which was consistently linked to dominant microbial hosts involved in key biological reactions for water purification. Finally, the high number of specific links detected between phages and bacterial species and the large proportion of lytic phages (77%) led to the conjecture that phages regulate bacterial populations through predation, preventing the proliferation of dominant species and contributing to the established functional redundancy among the dominant microbial groups. In conclusion, bacteriophages are likely to play a significant role in water treatment within biofilters, particularly through interactions with key bacterial species.

Effect of remediation reagents on bacterial composition and ecological function in black-odorous water sediments

Black-odorous urban water bodies and sediments pose a serious environmental problem. In this study, we conducted microcosm batch experiments to investigate the effect of remediation reagents (magnesium hydroxide and calcium nitrate) on native bacterial communities and their ecological functions in the black-odorous sediment of urban water. The dominant phyla (Proteobacteria, Actinobacteria, Chloroflexi, and Planctomycetes) and classes (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, Actinobacteria, Anaerolineae, and Planctomycetia) were determined under calcium nitrate and magnesium hydroxide treatments. Functional groups related to aerobic metabolism, including aerobic chemoheterotrophy, dark sulfide oxidation, and correlated dominant genera (Thiobacillus, Lysobacter, Gp16, and Gaiella) became more abundant under calcium nitrate treatment, whereas functional genes potentially involved in dissimilatory sulfate reduction became less abundant. The relative abundance of chloroplasts, fermentation, and correlated genera (Desulfomonile and unclassified Cyanobacteria) decreased under magnesium hydroxide treatment. Overall, these results indicated that calcium nitrate addition improved hypoxia-related reducing conditions in the sediment and promoted aerobic chemoheterotrophy.

The Coupling Response between Different Bacterial Metabolic Functions in Water and Sediment Improve the Ability to Mitigate Climate Change

Extreme climatic events, such as heat wave and large temperature fluctuations, are predicted to increase in frequency and intensity during the next hundred years, which may rapidly alter the composition and function of lake bacterial communities. Here, we conducted a year-long experiment to explore the effect of warming on bacterial metabolic function of lake water and sediment. Predictions of the metabolic capabilities of these communities were performed with FAPROTAX using 16S rRNA sequencing data. The results indicated that the increase in temperature changed the structure of bacterial metabolic functional groups in water and sediment. During periods of low temperature, the carbon degradation pathway decreased, and the synthesis pathway increased, under the stimulation of warming, especially under the conditions temperature fluctuation. We also observed that nitrogen fixation ability was especially important in the warming treatments during the summer season. However, an elevated temperature significantly led to reduced nitrogen fixation abilities in winter. Compared with the water column, the most predominant functional groups of nitrogen cycle in sediment were nitrite oxidation and nitrification. Variable warming significantly promoted nitrite oxidation and nitrification function in winter, and constant warming was significantly inhibited in spring, with control in sediments. Co-occurrence network results showed that warming, especially variable warming, made microbial co-occurrence networks larger, more connected and less modular, and eventually functional groups in the water column and sediment cooperated to resist warming. We concluded that warming changed bacterial functional potentials important to the biogeochemical cycling in the experimental mesocosms in winter and spring with low temperature. The effect of different bacteria metabolism functions in water column and sediment may change the carbon and nitrogen fluxes in aquatic ecosystems. In conclusion, the coupling response between different bacterial metabolic functions in water and sediment may improve the ability to mitigate climate change.

Linkage of community composition and function over short response time in anaerobic digestion systems with food fermentation wastewater

We investigated the short-term dynamics of microbial composition and function in bioreactors with inocula collected from full-scale and laboratory-based anaerobic digestion (AD) systems. The Bray-Curtis dissimilarity of both inocula was approximately 10% of the predicted Kyoto Encyclopedia of Genes and Genomes pathway and 40% of the taxonomic composition and yet resulted in a similar performance in methane production, implying that the variation of community composition may be decoupled from performance. However, the significant correlation of volatile fatty acids with taxonomic variation suggested that the pathways of AD could be different because of the varying genus. The predicted function of the significantly varying genus was mostly related to fermentation, which strengthened the conclusion that most microbial variation occurred within the fermentative species and led to alternative routes to result in similar methane production in methanogenic bioreactors. This finding sheds some light on the understanding of AD community regulation, which depends on the aims to recover intermediates or methane.

Bacteriophage-Mediated Control of Phytopathogenic Xanthomonads: A Promising Green Solution for the Future

Xanthomonads, members of the family Xanthomonadaceae, are economically important plant pathogenic bacteria responsible for infections of over 400 plant species. Bacteriophage-based biopesticides can provide an environmentally friendly, effective solution to control these bacteria. Bacteriophage-based biocontrol has important advantages over chemical pesticides, and treatment with these biopesticides is a minor intervention into the microflora. However, bacteriophages’ agricultural application has limitations rooted in these viruses’ biological properties as active substances. These disadvantageous features, together with the complicated registration process of bacteriophage-based biopesticides, means that there are few products available on the market. This review summarizes our knowledge of the Xanthomonas-host plant and bacteriophage-host bacterium interaction’s possible influence on bacteriophage-based biocontrol strategies and provides examples of greenhouse and field trials and products readily available in the EU and the USA. It also details the most important advantages and limitations of the agricultural application of bacteriophages. This paper also investigates the legal background and industrial property right issues of bacteriophage-based biopesticides. When appropriately applied, bacteriophages can provide a promising tool against xanthomonads, a possibility that is untapped. Information presented in this review aims to explore the potential of bacteriophage-based biopesticides in the control of xanthomonads in the future.

Metabolic modelling approaches for describing and engineering microbial communities

Microbes do not live in isolation but in microbial communities. The relevance of microbial communities is increasing due to growing awareness of their influence on a huge number of environmental, health and industrial processes. Hence, being able to control and engineer the output of both natural and synthetic communities would be of great interest. However, most of the available methods and biotechnological applications involving microorganisms, both in vivo and in silico, have been developed in the context of isolated microbes. In vivo microbial consortia development is extremely difficult and costly because it implies replicating suitable environments in the wet-lab. Computational approaches are thus a good, cost-effective alternative to study microbial communities, mainly via descriptive modelling, but also via engineering modelling. In this review we provide a detailed compilation of examples of engineered microbial communities and a comprehensive, historical revision of available computational metabolic modelling methods to better understand, and rationally engineer wild and synthetic microbial communities.

Effects of forced taxonomic transitions on metabolic composition and function in microbial microcosms

Surveys of microbial systems indicate that in many situations taxonomy and function may constitute largely independent ('decoupled') axes of variation. However, this decoupling is rarely explicitly tested experimentally, partly because it is hard to directly induce taxonomic variation without affecting functional composition. Here we experimentally evaluate this paradigm using microcosms resembling lake sediments and subjected to two different levels of salinity (0 and 19) and otherwise similar environmental conditions. We used DNA sequencing for taxonomic and functional profiling of bacteria and archaea and physicochemical measurements to monitor metabolic function, over 13 months. We found that the taxonomic composition of the saline systems gradually but strongly diverged from the fresh systems. In contrast, the metabolic composition (in terms of proportions of various genes) remained nearly identical across treatments and over time. Oxygen consumption rates and methane concentrations were substantially lower in the saline treatment, however, their similarity either increased (for oxygen) or did not change significantly (for methane) between the first and last sampling time, indicating that the lower metabolic activity in the saline treatments was directly and immediately caused by salinity rather than the gradual taxonomic divergence. Our experiment demonstrates that strong taxonomic shifts need not directly affect metabolic rates.

Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples

Metagenomics is a helpful tool for the analysis of unculturable organisms and viruses. Viruses that target bacteria and archaea play important roles in the microbial diversity of various ecosystems. Here we show that Methanosarcina virus MV (MetMV), the second Methanosarcina sp. virus with a completely determined genome, is characteristic of hydrocarbon pollution in environmental (soil and water) samples. It was highly abundant in Hungarian hydrocarbon polluted samples and its genome was also present in the NCBI SRA database containing reads from hydrocarbon polluted samples collected in Canada, indicating the stability of its niche and the marker feature of this virus. MetMV, as the only currently identified marker virus for pollution in environmental samples, could contribute to the understanding of the complicated network of prokaryotes and their viruses driving the decomposition of environmental pollutants.

Soil Bacterial Community Response and Nitrogen Cycling Variations Associated with Subalpine Meadow Degradation on the Loess Plateau, China

Grassland degradation is an ecological problem worldwide. This study aimed to reveal the patterns of the variations in bacterial diversity and community structure and in nitrogen cycling functional genes along a subalpine meadow degradation gradient on the Loess Plateau, China. Meadow degradation had a significant effect on the beta diversity of soil bacterial communities (P < 0.05) but not on the alpha diversity (P > 0.05). Nonmetric multidimensional scaling (NMDS) and analysis of similarity (ANOSIM) indicated that the compositions of bacterial and plant communities changed remarkably with increasing meadow degradation (all P < 0.05). The beta diversities of the plant and soil bacterial communities were significantly correlated (P < 0.05), while their alpha diversities were weakly correlated (P > 0.05) along the meadow degradation gradient. Redundancy analysis (RDA) showed that the structure of the bacterial community was strongly correlated with total nitrogen (TN), nitrate nitrogen (NO₃ ^--N), plant Shannon diversity, plant coverage, and soil bulk density (all P < 0.05). Moreover, the abundances of N fixation and denitrification genes of the bacterial community decreased along the degradation gradient, but the abundance of nitrification genes increased along the gradient. The structure of the set of N cycling genes present at each site was more sensitive to subalpine meadow degradation than the structure of the total bacterial community. Our findings revealed compositional shifts in the plant and bacterial communities and in the abundances of key N cycling genes as well as the potential drivers of these shifts under different degrees of subalpine meadow degradation.IMPORTANCE Soil microbes play a crucial role in the biogeochemical cycles of grassland ecosystems, yet information on how their community structure and functional characteristics change with subalpine meadow degradation is scarce. In this study, we evaluated the changes in bacterial community structure and nitrogen functional genes in degraded meadow soils. Meadow degradation had a significant effect on bacterial community composition. Soil total nitrogen was the best predictor of bacterial community structure. The beta diversities of the plant and soil bacterial communities were significantly correlated, while their alpha diversities were only weakly correlated. Meadow degradation decreased the potential for nitrogen fixation and denitrification but increased the potential for nitrification. These results have implications for the restoration and reconstruction of subalpine meadow ecosystem on the Loess Plateau.

Urbanization drives riverine bacterial antibiotic resistome more than taxonomic community at watershed scale

Although the occurrence and distribution of antibiotic resistance genes (ARGs) in various aquatic ecosystems are well explored, understanding of the ecological processes and mechanisms governing the composition and dynamics of bacterial ARGs still remains limited across space and time. Here, we used high-throughput approaches to detect spatial patterns of bacterial ARGs and operational taxonomic units (OTUs) in an urbanizing subtropical watershed, Xiamen, southeast China over a five-year period. At watershed scale, the OTU profiles were undergoing a directional change, but the ARG profiles showed a high stability or stochastic change over time. Compared with the upstream and midstream, the richness, absolute abundance, normalized abundance and diversity of ARGs were significantly higher in the downstream waters. Our results revealed a clear rural-urban disparity in ARG and OTU profiles which were mainly governed by deterministic and stochastic assembly processes, respectively. With the increase of urban building area along the river, the ecological processes of ARG profiles shifted from stochastic to deterministic. In downstream waters, the bacterial ARG profiles were much more stable than bacterial OTUs. Further, our results indicated that both human-dominated environment (e.g., land use) and mobile genetic elements (MGEs) played an important role in shaping the ARG profiles and dynamics. Overall, this was a response to spatially extensive human-landscape interactions that included urban development in the river downstream region, which were common across subtropical coastal cities of China and can alter the ARG profile dynamics along rural-urban gradient. Therefore, watershed management actions aiming at reducing threats posed by ARGs in urbanizing watershed should first consider the surrounding urbanization level and the mode and intensity of human activity. Our findings also imply that due to the decoupling of bacterial function and taxonomy, both aspects should be studied separately.

Rumen Virus Populations: Technological Advances Enhancing Current Understanding

The rumen contains a multi-kingdom, commensal microbiome, including protozoa, bacteria, archaea, fungi and viruses, which enables ruminant herbivores to ferment and utilize plant feedstuffs that would be otherwise indigestible. Within the rumen, virus populations are diverse and highly abundant, often out-numbering the microbial populations that they both predate on and co-exist with. To date the research effort devoted to understanding rumen-associated viral populations has been considerably less than that given to the other microbial populations, yet their contribution to maintaining microbial population balance, intra-ruminal microbial lysis, fiber breakdown, nutrient cycling and genetic transfer may be highly significant. This review follows the technological advances which have contributed to our current understanding of rumen viruses and drawing on knowledge from other environmental and animal-associated microbiomes, describes the known and potential roles and impacts viruses have on rumen function and speculates on the future directions of rumen viral research.

Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages

BACKGROUND

It remains unclear whether adaptation and changes in diversity associated to a long-term perturbation are sufficient to ensure functional resilience of soil microbial communities. We used RNA-based approaches (16S rRNA gene transcript amplicon coupled to shotgun mRNA sequencing) to study the legacy effects of a century-long soil copper (Cu) pollution on microbial activity and composition, as well as its effect on the capacity of the microbial community to react to temporal fluctuations.

RESULTS

Despite evidence of microbial adaptation (e.g., iron homeostasis and avoidance/resistance strategies), increased heterogeneity and richness loss in transcribed gene pools were observed with increasing soil Cu, together with an unexpected predominance of phage mRNA signatures. Apparently, phage activation was either triggered directly by Cu, or indirectly via enhanced expression of DNA repair/SOS response systems in Cu-exposed bacteria. Even though total soil carbon and nitrogen had accumulated with increasing Cu, a reduction in temporally induced mRNA functions was observed. Microbial temporal response groups (TRGs, groups of microbes with a specific temporal response) were heavily affected by Cu, both in abundance and phylogenetic composition.

CONCLUSION

Altogether, results point toward a Cu-mediated "decoupling" between environmental fluctuations and microbial activity, where Cu-exposed microbes stopped fulfilling their expected contributions to soil functioning relative to the control. Nevertheless, some functions remained active in February despite Cu, concomitant with an increase in phage mRNA signatures, highlighting that somehow, microbial activity is still happening under these adverse conditions.

Response of environmental variables and microbial community to sodium percarbonate addition to contaminated sediment

Sodium percarbonate (SPC) is a common reagent used for in situ remediation of contaminated soil. Current studies focus on the effects of SPC on pollutant removal; however, a knowledge gap exists for the biochemical process following SPC addition. In this study, a microcosm batch experiment was conducted to investigate the residual effect caused by different doses of SPC addition on native microbial communities, as well as on the environmental variables of contaminated sediments. The obtained results showed that the more SPC was added, the more dissolved matters were generated and the oxidation-reduction potential was lowered. Furthermore, the metabolic activities of the microbial community were enhanced and the microbial community structure responded differently to different SPC doses: the microbes that increased at high SPC dose mainly belonged to the phylum Firmicutes, the class Clostridia, and the genera Petrimonas and Proteiniclasticum. The microbes that increased at medium SPC dose mainly belonged to the class Alphaproteobacteria and the genus Brevundimonas. In contrast, vulnerable microbes mainly belonged to the phylum Acidobacteria, the class Caldisericia, Holophagae, and the genus Sulfuricurvum. Microbes capable of fermentation, ureolysis, and chemohetrotrophy increased. These results indicate that SPC addition could indirectly provide both electron acceptors and donors, thus improving the metabolic activities of the microorganisms in the contaminated sediment. Furthermore, the utilized SPC dose should be considered to achieve the optimal benefit for in situ remediation. This study forms a valuable reference for the application of SPC in ecological engineering.

Function and functional redundancy in microbial systems

Microbial communities often exhibit incredible taxonomic diversity, raising questions regarding the mechanisms enabling species coexistence and the role of this diversity in community functioning. On the one hand, many coexisting but taxonomically distinct microorganisms can encode the same energy-yielding metabolic functions, and this functional redundancy contrasts with the expectation that species should occupy distinct metabolic niches. On the other hand, the identity of taxa encoding each function can vary substantially across space or time with little effect on the function, and this taxonomic variability is frequently thought to result from ecological drift between equivalent organisms. Here, we synthesize the powerful paradigm emerging from these two patterns, connecting the roles of function, functional redundancy and taxonomy in microbial systems. We conclude that both patterns are unlikely to be the result of ecological drift, but are inevitable emergent properties of open microbial systems resulting mainly from biotic interactions and environmental and spatial processes.

Coevolution Maintains Diversity in the Stochastic "Kill the Winner" Model

The "kill the winner" hypothesis is an attempt to address the problem of diversity in biology. It argues that host-specific predators control the population of each prey, preventing a winner from emerging and thus maintaining the coexistence of all species in the system. We develop a stochastic model for the kill the winner paradigm and show that the stable coexistence state of the deterministic kill the winner model is destroyed by demographic stochasticity, through a cascade of extinction events. We formulate an individual-level stochastic model in which predator-prey coevolution promotes the high diversity of the ecosystem by generating a persistent population flux of species.