Multifunctionality and diversity in bacterial biofilms

Selection of aquatic microbiota exposed to the herbicides flufenacet and metazachlor

Herbicides are important, ubiquitous environmental contaminants, but little is known about their interaction with bacterial aquatic communities. Here, we sampled a protected natural freshwater habitat and characterised its microbiome in interaction with herbicides. We evolved the freshwater microbiomes in a microcosm assay of exposure (28 days) to flufenacet and metazachlor at environmental concentrations of 0.5, 5 and 50 μg L-1 . Inhibitory effects of herbicides were exemplarily assessed in cultured bacteria from the same pond (Pseudomonas alcaligenes, Paenibacillus amylolyticus and Microbacterium hominis). Findings were compared to long-term concentrations as provided by local authorities. Here, environmental concentrations reached up to 11 μg L-1 (flufenacet) and 76 μg L-1 (metazachlor). Bacteria were inhibited at minimum inhibitory concentrations far above these values; however, concentrations of 50 μg L-1 of flufenacet resulted in measurable growth impairment. While most herbicide-exposed microcosm assays did not differ from controls, Acidobacteria were selected at high environmental concentrations of herbicides. Alpha-diversity (e.g., taxonomic richness on phylum level) was reduced when aquatic microbiomes were exposed to 50 μg metazachlor or flufenacet. One environmental strain of P. alcaligenes showed resistance to high concentrations of flufenacet (50 g L-1 ). In total, this study reveals that ecologic imbalance due to herbicide use significantly impacts aquatic microbiomes.

Multifunctional redundancy: Impossible or undetected?

The diversity-functioning relationship is a pillar of ecology. Two significant concepts have emerged from this relationship: redundancy, the asymptotic relationship between diversity and functioning, and multifunctionality, a monotonic relationship between diversity and multiple functions occurring simultaneously. However, multifunctional redundancy, an asymptotic relationship between diversity and multiple functions occurring simultaneously, is rarely detected in research. Here we assess whether this lack of detection is due to its true rarity, or due to systematic research error. We discuss how inconsistencies in the use of terms such as 'function' lead to mismatched research. We consider the different techniques used to calculate multifunctionality and point out a rarely considered issue: how determining a function's maximum rate affects multifunctionality metrics. Lastly, we critique how a lack of consideration of multitrophic, spatiotemporal, interactions and community assembly processes in designed experiments significantly reduces the likelihood of detecting multifunctional redundancy. Multifunctionality research up to this stage has made significant contributions to our understanding of the diversity-functioning relationship, and we believe that multifunctional redundancy is detectable with the use of appropriate methodologies.

Microplastics as an emerging menace to environment: Insights into their uptake, prevalence, fate, and sustainable solutions

The inflated demand for plastic products has led to tremendous rise in plastic debris in different environmental matrices, thereby resulting in plastic pollution. This affects plants, animals, and even humans, as microplastics can enter the food chain and cause several health implications. Microplastics are the small plastic particles (size below 5 mm) that are largely debated nowadays owing to their environmental risk assessment. Their potential to interact with other toxic contaminants, their tendency to be ingested or taken up by living organisms and their longevity is a serious threat to our environment. However, despite wealth of recent information, still there is a gap, particularly in eco-toxicology studies, fate, prevalence and feasible solutions to cope up with the menace of microplastics pollution. This review unravels the environmental fate and behaviour of microplastics as well as their global distribution in the marine and terrestrial environment. Furthermore, we aim to contribute to the international debate on the microplastics global paradigm. We briefly suggest sustainable solutions and recommendations to achieve future research goals on microplastics. Our review reveals some of the newest biological (green algae and modified sponges) and physical (nano-particles and membrane treatment) remediation solutions to eradicate microplastics from different types of environment. This review presents a critical evaluation of the state of knowledge of micro-plastics and suggested some recommendations which can help in identifying some important key questions for future research.

Ecotoxicological and health implications of microplastic-associated biofilms: a recent review and prospect for turning the hazards into benefits

Microplastics (MPs), over the years, have been regarded as a severe environmental nuisance with adverse effects on our ecosystem as well as human health globally. In recent times, microplastics have been reported to support biofouling by genetically diverse organisms resulting in the formation of biofilms. Biofilms, however, could result in changes in the physicochemical properties of microplastics, such as their buoyancy and roughness. Many scholars perceived the microplastic-biofilm association as having more severe consequences, providing evidence of its effects on the environment, aquatic life, and nutrient cycles. Furthermore, other researchers have shown that microplastic-associated biofilms have severe consequences on human health as they serve as vectors of heavy metals, toxic chemicals, and antibiotic resistance genes. Despite what is already known about their adverse effects, other interesting avenues are yet to be fully explored or developed to turn the perceived negative microplastic-biofilm association to our advantage. The major inclusion criteria for relevant literature were that it must focus on microplastic association biofilms, while we excluded papers solely on biofilms or microplastics. A total of 242 scientific records were obtained. More than 90% focused on explaining the environmental and health impacts of microplastic-biofilm association, whereas only very few studies have reported the possibilities and opportunities in turning the microplastic biofilms association into benefits. In summary, this paper concisely reviews the current knowledge of microplastic-associated biofilms and their adverse consequences and further proposes some approaches that can be developed to turn the negative association into positive.

Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms

The resistance and resilience provided by functional redundancy, a common feature of microbial communities, is not always advantageous. An example is nitrite oxidation in partial nitritation-anammox (PNA) reactors designed for nitrogen removal in wastewater treatment, where suppression of nitrite oxidizers like Nitrospira is sought. In these ecosystems, biofilms provide microhabitats with oxygen gradients, allowing the coexistence of aerobic and anaerobic bacteria. We designed a disturbance experiment where PNA biofilms, treating water from a high-rate activated sludge process, were constantly or intermittently exposed to anaerobic sidestream wastewater, which has been proposed to inhibit nitrite oxidizers. With increasing sidestream exposure we observed decreased abundance, alpha-diversity, functional versatility, and hence functional redundancy, among Nitrospira in the PNA biofilms, while the opposite patterns were observed for anammox bacteria within Brocadia. At the same time, species turnover was observed for aerobic ammonia-oxidizing Nitrosomonas populations. The different exposure regimens were associated with metagenomic assembled genomes of Nitrosomonas, Nitrospira, and Brocadia, encoding genes related to N-cycling, substrate usage, and osmotic stress response, possibly explaining the three different patterns by niche differentiation. These findings imply that disturbances can be used to manage the functional redundancy of biofilm microbiomes in a desirable direction, which should be considered when designing operational strategies for wastewater treatment.

New index of functional specificity to predict the redundancy of ecosystem functions in microbial communities

An ecosystem function is suggested to be more sensitive to biodiversity loss (i.e. low functional redundancy) when focusing on specific-type functions than broad-type functions. Thus far, specific-type functions have been loosely defined as functions performed by a small number of species (facilitative species) or functions involved in utilizing complex substrates. However, quantitative examination of functional specificity remains underexplored. We quantified the functional redundancy of 33 ecosystem functions in a freshwater system from 76 prokaryotic community samples over three years. For each function, we used a sparse regression model to estimate the number of facilitative Amplicon Sequence Variants (ASVs) and to define taxon-based functional specificity. We also used Bertz structural complexity to determine substrate-based functional specificity. We found that functional redundancy increased with the taxon-based functional specificity defined as the proportion of facilitative ASVs ( = facilitative ASV richness/ facilitative ASV richness + repressive ASV (ASVs reducing functioning) richness). When using substrate-based functional specificity, functional redundancy was influenced by Bertz complexity per se and by substrate acquisition mechanisms. Therefore, taxon-based functional specificity is a better predictive index for evaluating functional redundancy than substrate-based functional specificity. These findings provide a framework to quantitatively predict the consequences of diversity losses on ecosystem functioning.

The impact of microplastic-microbe interactions on animal health and biogeochemical cycles: A mini-review

Microplastic (MP) pollution has attracted global attention due to the extensive use of plastic products. The hydrophobic MP surface provides a habitat for multiple microorganisms. Although there have been several studies on the impact of plastic particles on microbial communities, there are few reviews that have systematically summarized the interaction between MPs and microbes and their effects on human health and biochemical circulation. The discussions in this review will take place under the following topics: (1) MPs prompt colonization, biofilm generation, and transfer of environmental microbes; (2) the microbial communities can cause the morphological alterations and biodegradation of MPs; (3) MP-microbe combinations can induce the alteration of intestinal flora and hazard animal health; (4) the biogeochemical cycles affected by MP-microbe interactions. This review will highlight the close interactions between MPs and microorganisms, and provide suggestions for future studies.

Environmental Parameters and Substrate Type Drive Microeukaryotic Community Structure During Short-Term Experimental Colonization in Subtropical Eutrophic Freshwaters

Microeukaryotes are key components of aquatic ecosystems and play crucial roles in aquatic food webs. However, influencing factors and potential assembly mechanisms for microeukaryotic community on biofilms are rarely studied. Here, those of microeukaryotic biofilms in subtropical eutrophic freshwaters were investigated for the first time based on 2,585 operational taxonomic units (OTUs) from 41 samples, across different environmental conditions and substrate types. Following conclusions were drawn: (1) Environmental parameters were more important than substrate types in structuring microeukaryotic community of biofilms in subtropical eutrophic freshwaters. (2) In the fluctuating river, there was a higher diversity of OTUs and less predictability of community composition than in the stable lake. Sessile species were more likely to be enriched on smooth surfaces of glass slides, while both free-swimming and attached organisms occurred within holes inside PFUs (polyurethane foam units). (3) Both species sorting and neutral process were mechanisms for assembly of microeukaryotic biofilms, but their importance varied depending on different habitats and substrates. (4) The effect of species sorting was slightly higher than the neutral process in river biofilms due to stronger environmental filtering. Species sorting was a stronger force structuring communities on glass slides than PFUs with more niche availability. Our study sheds light on assembly mechanisms for microeukaryotic community on different habitat and substrate types, showing that the resulting communities are determined by both sets of variables, in this case primarily habitat type. The balance of neutral process and species sorting differed between habitats, but the high alpha diversity of microeukaryotes in both led to similar sets of lifecycle traits being selected for in each case.

Seasonal Water Level Fluctuation and Concomitant Change of Nutrients Shift Microeukaryotic Communities in a Shallow Lake

Seasonal water level fluctuations (WLFs) impose dramatic influences on lake ecosystems. The influences of WLFs have been well studied for many lake biotas but the microeukaryotic community remains one of the least-explored features. This study employed high-throughput 18S rRNA gene sequencing to investigate the spatiotemporal patterns of microeukaryotic communities in the dry and wet seasons with concomitant change of nutrients in Poyang Lake, which experiences huge seasonal WLFs. The results showed that the dry season and wet season had distinct microeukaryotic community compositions and structures. In the dry season, Ciliophora (13.86–40.98%) and Cryptomonas (3.69–18.64%) were the dominant taxa, and the relative abundance of these taxa were significant higher in the dry season than wet season. Ochrophyta (6.88–45.67%) and Chlorophyta (6.31–22.10%) was the dominant taxa of microeukaryotic communities in the wet season. The seasonal variation of microeukaryotic communities was strongly correlated to seasonal nutrient variations. Microeukaryotic communities responded significantly to dissolved organic carbon, total nitrogen, nitrate, and soluble reactive phosphorus in the dry season, and correlated to nitrate and total phosphorus in the wet season. The microeukaryotic community showed different modular structures in two seasons, and nutrient variations were the key factors influencing seasonal variations of the modular structures. Moreover, microeukaryotic community networks based on different seasons indicated that the microeukaryotic community co-occurrence patterns were not constant but varied largely associating with the nitrogen and phosphorus variations under the effects of WLFs. Our results are important for understanding how microeukaryotic communities respond to nutrient variation under seasonal water level fluctuation.

Reservoir water stratification and mixing affects microbial community structure and functional community composition in a stratified drinking reservoir

To investigate how the aquatic bacterial community of a stratified reservoir drives the evolution of water parameters, the microbial community structure and network characteristics of bacteria in a stratified reservoir were investigated using Illumina MiSeq sequencing technology. A total of 42 phyla and 689 distinct genera were identified, which showed significant seasonal variation. Additionally, stratified variations in the bacterial community strongly reflected the vertical gradient and seasonal changes in water temperature, dissolved oxygen, and nutrition concentration. Furthermore, principal coordinate analysis indicated that most microorganisms were likely influenced by changes in water stratification conditions, exhibiting significant differences during the stratification period and mixing period based on Adonis, MRPP, and Anosim. Compared to the stratification period, 123 enhanced operational taxonomic units (OTUs; 29%) and 226 depleted OTUs (52%) were identified during the mixing period. Linear discriminant analysis effect size results showed that 15 major genera were enriched in the mixing period and 10 major genera were enriched in the stratification period. Importantly, network analysis revealed that the keystone species belonged to hgcI_clade, CL500-29, Acidibacter, Paucimonas, Flavobacterium, Prochlorothrix, Xanthomonadales, Chloroflexia, Burkholderiales, OPB56, KI89A_clade, Synechococcus, Caulobacter or were unclassified. Redundancy analysis showed that temperature, dissolved oxygen, pH, chlorophyll-α, total phosphorus, nitrate, and ammonia were important factors influencing the water bacterial community and function composition, which were consistent with the results of the Mantel test analysis. Furthermore, random forest analysis showed that temperature, dissolved oxygen, ammonia, and total dissolved phosphorous were the most important variables predicting water bacterial community and function community α- and β-diversity (P < 0.05). Overall, these results provide insight into the interactions between the microbial community and water quality evolution mechanism in Zhoucun reservoir.

Headwater Stream Microbial Diversity and Function across Agricultural and Urban Land Use Gradients

Anthropogenic activity impacts stream ecosystems, resulting in a loss of diversity and ecosystem function; however, little is known about the response of aquatic microbial communities to changes in land use. Here, microbial communities were characterized in 82 headwater streams across a gradient of urban and agricultural land uses using 16S rRNA gene amplicon sequencing and compared to a rich data set of physicochemical variables and traditional benthic invertebrate indicators. Microbial diversity and community structures differed among watersheds with high agricultural, urban, and forested land uses, and community structure differed in streams classified as being in good, fair, poor, and very poor condition using benthic invertebrate indicators. Microbial community similarity decayed with geodesic distance across the study region but not with environmental distance. Stream community respiration rates ranged from 21.7 to 1,570 mg O₂ m^-2 day^-1 and 31.9 to 3,670 mg O₂ m^-2 day^-1 for water column and sediments, respectively, and correlated with nutrients associated with anthropogenic influence and microbial community structure. Nitrous oxide (N₂O) concentrations ranged from 0.22 to 4.41 μg N₂O liter^-1; N₂O concentration was negatively correlated with forested land use and was positively correlated with dissolved inorganic nitrogen concentrations. Our findings suggest that stream microbial communities are impacted by watershed land use and can potentially be used to assess ecosystem health.IMPORTANCE Stream ecosystems are frequently impacted by changes in watershed land use, resulting in altered hydrology, increased pollutant and nutrient loads, and habitat degradation. Macroinvertebrates and fish are strongly affected by changes in stream conditions and are commonly used in biotic indices to assess ecosystem health. Similarly, microbes respond to environmental stressors, and changes in community composition alter key ecosystem processes. The response of microbes to habitat degradation and their role in global biogeochemical cycles provide an opportunity to use microbes as a monitoring tool. Here, we identify stream microbes that respond to watershed urbanization and agricultural development and demonstrate that microbial diversity and community structure can be used to assess stream conditions and ecosystem functioning.

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences

BACKGROUND

Sequencing of 16S rRNA genes has become a powerful technique to study microbial communities and their responses towards changing environmental conditions in various ecosystems. Several tools have been developed for the prediction of functional profiles from 16S rRNA gene sequencing data, because numerous questions in ecosystem ecology require knowledge of community functions in addition to taxonomic composition. However, the accuracy of these tools relies on functional information derived from genomes available in public databases, which are often not representative of the microorganisms present in the studied ecosystem. In addition, there is also a lack of tools to predict functional gene redundancy in microbial communities.

RESULTS

To address these challenges, we developed Tax4Fun2, an R package for the prediction of functional profiles and functional gene redundancies of prokaryotic communities from 16S rRNA gene sequences. We demonstrate that functional profiles predicted by Tax4Fun2 are highly correlated to functional profiles derived from metagenomes of the same samples. We further show that Tax4Fun2 has higher accuracies than PICRUSt and Tax4Fun. By incorporating user-defined, habitat-specific genomic information, the accuracy and robustness of predicted functional profiles is substantially enhanced. In addition, functional gene redundancies predicted with Tax4Fun2 are highly correlated to functional gene redundancies determined for simulated microbial communities.

CONCLUSIONS

Tax4Fun2 provides researchers with a unique tool to predict and investigate functional profiles of prokaryotic communities based on 16S rRNA gene sequencing data. It is easy-to-use, platform-independent and highly memory-efficient, thus enabling researchers without extensive bioinformatics knowledge or access to high-performance clusters to predict functional profiles. Another unique feature of Tax4Fun2 is that it allows researchers to calculate the redundancy of specific functions, which is a potentially important measure of how resilient a community will be to environmental perturbation. Tax4Fun2 is implemented in R and freely available at https://github.com/bwemheu/Tax4Fun2.

Impact of Nutrient and Stoichiometry Gradients on Microbial Assemblages in Erhai Lake and Its Input Streams

Networks of lakes and streams are linked by downslope flows of material and energy within catchments. Understanding how bacterial assemblages are associated with nutrients and stoichiometric gradients in lakes and streams is essential for understanding biogeochemical cycling in freshwater ecosystems. In this study, we conducted field sampling of bacterial communities from lake water and stream biofilms in Erhai Lake watershed. We determined bacterial communities using high-throughput 16S rRNA gene sequencing and explored the relationship between bacterial composition and environmental factors using networking analysis, canonical correspondence analysis (CCA), and variation partitioning analysis (VPA). Physicochemical parameters, nutrients, and nutrient ratios gradients between the lake and the streams were strongly associated with the differences in community composition and the dominant taxa. Cyanobacteria dominated in Erhai Lake, while Proteobacteria dominated in streams. The stream bacterial network was more stable with multiple stressors, including physicochemical-factors and nutrient-factors, while the lake bacterial network was more fragile and susceptible to human activities with dominant nutrients (phosphorus). Negative correlations between bacterial communities and soluble reactive phosphorus (SRP) as well as positive correlations between bacterial communities and dissolved organic carbon (DOC) in the network indicated these factors had strong effect on bacterial succession. Erhai Lake is in a eutrophic state, and high relative abundances of Synechococcus (40.62%) and Microcystis (16.2%) were noted during the course of our study. CCA indicated that nutrients (phosphorus) were key parameters driving Cyanobacteria-dominated community structure. By classifying the environmental factors into five categories, VPA analyses identified that P-factor (total phosphorus (TP) and SRP) as well as the synergistic effect of C-factor (DOC), N-factor (NO3−), and P-factor (TP and SRP) played a central role in structuring the bacterial communities in Erhai Lake. Heterogeneous physicochemical conditions explained the variations in bacterial assemblages in streams. This study provides a picture of stream–lake linkages from the perspective of bacterial community structure as well as key factors driving bacterial assemblages within lakes and streams at the whole watershed scale. We further argue that better management of phosphorus on the watershed scale is needed for ameliorating eutrophication of Erhai Lake.

Distinct Bacterial Communities in Wet and Dry Seasons During a Seasonal Water Level Fluctuation in the Largest Freshwater Lake (Poyang Lake) in China

Water level fluctuations (WLFs) are an inherent feature of lake ecosystems and have been regarded as a pervasive pressure on lacustrine ecosystems globally due to anthropogenic activities and climate change. However, the impacts of WLFs on lake microbial communities is one of our knowledge gaps. Here, we used the high-throughput 16S rRNA gene sequencing approach to investigate the taxonomic and functional dynamics of bacterial communities in wet-season and dry-season of Poyang Lake (PYL) in China. The results showed that dry-season was enriched in total nitrogen (TN), nitrate (NO3 -), ammonia (NH4 +), and soluble reactive phosphorus (SRP), while wet-season was enriched in dissolved organic carbon (DOC) and total phosphorus (TP). Bacterial communities were distinct taxonomically and functionally in dry-season and wet-season and the nutrients especially P variation had a significant contribution to the seasonal variation of bacterial communities. Moreover, bacterial communities responded differently to nutrient dynamics in different seasons. DOC, NO3 -, and SRP had strong influences on bacterial communities in dry-season while only TP in wet-season. Alpha-diversity, functional redundancy, taxonomic dissimilarities, and taxa niche width were higher in dry-season, while functional dissimilarities were higher in wet-season, suggesting that the bacterial communities were more taxonomically sensitive in dry-season while more functionally sensitive in wet-season. Bacterial communities were more efficient in nutrients utilization in wet-season and might have different nitrogen removal mechanisms in different seasons. Bacterial communities in wet-season had significantly higher relative abundance of denitrification genes but lower anammox genes than in dry-season. This study enriched our knowledge of the impacts of WLFs and seasonal dynamics of lake ecosystems. Given the increasingly pervasive pressure of WLFs on lake ecosystems worldwide, our findings have important implications for conservation and management of lake ecosystems.

Biofilm growth and control in cooling water industrial systems

Matrix-embedded, surface-attached microbial communities, known as biofilms, profusely colonise industrial cooling water systems, where the availability of nutrients and organic matter favours rapid microbial proliferation and their adhesion to surfaces in the evaporative fill material, heat exchangers, water reservoir and cooling water sections and pipelines. The extensive growth of biofilms can promote micro-biofouling and microbially induced corrosion (MIC) as well as pose health problems associated with the presence of pathogens like Legionella pneumophila. This review examines critically biofilm occurrence in cooling water systems and the main factors potentially affecting biofilm growth, biodiversity and structure. A broad evaluation of the most relevant biofilm monitoring and control strategies currently used or potentially useful in cooling water systems is also provided.

Understanding urban stormwater denitrification in bioretention internal water storage zones

Conventional free-draining bioretention systems promote nitrate production and continual leaching to receiving waters. In this study, laboratory tests demonstrated the efficacy of an internal water storage zone (IWSZ) to target nitrate removal via denitrification. Experimental results confirmed that the carbon substrate characteristics (Willow Oak woodchip media) and the hydraulic retention time of nitrified stormwater affected nitrate removal performance. A 2.6-day batch treatment time reduced 3.0 mg-N/L to <0.01 mg/L, corresponding to a first-order denitrification rate constant of 0.0011 min^-1 . Under various flow conditions, the associated hydraulic retention time may be used as a predictive measurement of nitrate removal performance. Scanning electron microscopy and 16S rRNA analysis of the woodchips showed that biofilms were present that could be responsible for anaerobic lignocellulose degradation and denitrification. This knowledge, along with evaluation of the biofilm community composition, reinforced the notion of a heterogeneous structure due to nutrient availability and hydrodynamic conditions. PRACTITIONER POINTS: Denitrification can occur using woodchips in a bioretention internal water storage zone. The denitrification rate is slow and may be limited during field-scale applications. A woodchip pretreatment did not provide long-term enhancement to the denitrification rate. Denitrification bacteria were found in the internal water storage zone.

Matrix Polysaccharides and SiaD Diguanylate Cyclase Alter Community Structure and Competitiveness of Pseudomonas aeruginosa during Dual-Species Biofilm Development with Staphylococcus aureus

Bacteria in natural and engineered environments form biofilms that include many different species. Microorganisms rely on a number of different strategies to manage social interactions with other species and to access resources, build biofilm consortia, and optimize growth. For example, Pseudomonas aeruginosa and Staphylococcus aureus are biofilm-forming bacteria that coinfect the lungs of cystic fibrosis patients and diabetic and chronic wounds. P. aeruginosa is known to antagonize S. aureus growth. However, many of the factors responsible for mixed-species interactions and outcomes such as infections are poorly understood. Biofilm bacteria are encased in a self-produced extracellular matrix that facilitates interspecies behavior and biofilm development. In this study, we examined the poorly understood roles of the major matrix biopolymers and their regulators in mixed-species biofilm interactions and development.

Mixed-species biofilms display a number of emergent properties, including enhanced antimicrobial tolerance and communal metabolism. These properties may depend on interspecies relationships and the structure of the biofilm. However, the contribution of specific matrix components to emergent properties of mixed-species biofilms remains poorly understood. Using a dual-species biofilm community formed by the opportunistic pathogens Pseudomonas aeruginosa and Staphylococcus aureus, we found that whilst neither Pel nor Psl polysaccharides, produced by P. aeruginosa, affect relative species abundance in mature P. aeruginosa and S. aureus biofilms, Psl production is associated with increased P. aeruginosa abundance and reduced S. aureus aggregation in the early stages of biofilm formation. Our data suggest that the competitive effect of Psl is not associated with its structural role in cross-linking the matrix and adhering to P. aeruginosa cells but is instead mediated through the activation of the diguanylate cyclase SiaD. This regulatory control was also found to be independent of the siderophore pyoverdine and Pseudomonas quinolone signal, which have previously been proposed to reduce S. aureus viability by inducing lactic acid fermentation-based growth. In contrast to the effect mediated by Psl, Pel reduced the effective crosslinking of the biofilm matrix and facilitated superdiffusivity in microcolony regions. These changes in matrix cross-linking enhance biofilm surface spreading and expansion of microcolonies in the later stages of biofilm development, improving overall dual-species biofilm growth and increasing biovolume severalfold. Thus, the biofilm matrix and regulators associated with matrix production play essential roles in mixed-species biofilm interactions.

Monitoring biofilm function in new and matured full-scale slow sand filters using flow cytometric histogram image comparison (CHIC)

While slow sand filters (SSFs) have produced drinking water for more than a hundred years, understanding of their associated microbial communities is limited. In this study, bacteria in influent and effluent water from full-scale SSFs were explored using flow cytometry (FCM) with cytometric histogram image comparison (CHIC) analysis; and routine microbial counts for heterotrophs, total coliforms and Escherichia coli. To assess if FCM can monitor biofilm function, SSFs differing in age and sand composition were compared. FCM profiles from two established filters were indistinguishable. To examine biofilm in the deep sand bed, SSFs were monitored during a scraping event, when the top layer of sand and the schmutzdecke are removed to restore flow through the filter. The performance of an established SSF was stable: total organic carbon (TOC), pH, numbers of heterotrophs, coliforms, E. coli, and FCM bacterial profile were unaffected by scraping. However, the performance of two newly-built SSFs containing new and mixed sand was compromised: breakthrough of both microbial indicators and TOC occurred following scraping. The compromised performance of the new SSFs was reflected in distinct effluent bacterial communities; and, the presence of microbial indicators correlated to influent bacterial communities. This demonstrated that FCM can monitor SSF performance. Removal of the top layer of sand did not alter the effluent water from the established SSF, but did affect that of the SSFs containing new sand. This suggests that the impact of the surface biofilm on effluent water is greater when the deep sand bed biofilm is not established.

Taxa-function robustness in microbial communities

BACKGROUND

The species composition of a microbial community is rarely fixed and often experiences fluctuations of varying degrees and at varying frequencies. These perturbations to a community's taxonomic profile naturally also alter the community's functional profile-the aggregate set of genes encoded by community members-ultimately altering the community's overall functional capacities. The magnitude of such functional changes and the specific shift that will occur in each function, however, are strongly dependent on how genes are distributed across community members' genomes. This gene distribution, in turn, is determined by the taxonomic composition of the community and would markedly differ, for example, between communities composed of species with similar genomic content vs. communities composed of species whose genomes encode relatively distinct gene sets. Combined, these observations suggest that community functional robustness to taxonomic perturbations could vary widely across communities with different compositions, yet, to date, a systematic study of the inherent link between community composition and robustness is lacking.

RESULTS

In this study, we examined how a community's taxonomic composition influences the robustness of that community's functional profile to taxonomic perturbation (here termed taxa-function robustness) across a wide array of environments. Using a novel simulation-based computational model to quantify this taxa-function robustness in host-associated and non-host-associated communities, we find notable differences in robustness between communities inhabiting different body sites, including significantly higher robustness in gut communities compared to vaginal communities that cannot be attributed solely to differences in species richness. We additionally find between-site differences in the robustness of specific functions, some of which are potentially related to site-specific environmental conditions. These taxa-function robustness differences are most strongly associated with differences in overall functional redundancy, though other aspects of gene distribution also influence taxa-function robustness in certain body environments, and are sufficient to cluster communities by environment. Further analysis revealed a correspondence between our robustness estimates and taxonomic and functional shifts observed across human-associated communities.

CONCLUSIONS

Our analysis approach revealed intriguing taxa-function robustness variation across environments and identified features of community and gene distribution that impact robustness. This approach could be further applied for estimating taxa-function robustness in novel communities and for informing the design of synthetic communities with specific robustness requirements.

In the ovary of Ciona intestinalis (Type A), immune-related galectin and phenoloxidase genes are differentially expressed by the follicle accessory cells

Riboprobes (in situ hybridization) and antibodies (immunohistochemistry), previously used to show the upregulation of Ciona intestinalis (Type A) galectins (CiLgals-a, CiLgals-b) and phenoloxidase (CinPO2) immune-related genes, were tested on histological sections of the ovary. The ovarian follicles are composed of oocytes encased by follicular cells (FCs) and test cells (TCs). Results show the transcription upregulation of both CiLgals and CinPO2 genes in the vitellogenic FCs, conversely distinct cytolocalization of the proteins are shown. At vitellogenic stage, the CiLgals are localized in the FCs, in the oocyte cytoplasm, and close to the germinal vesicle (GV), whereas the CinPO2 was never identified in the FCs. In a presumptive advanced phase and at the post-vitellogenic stage the TCs appear to be labelled by the CinPO2 riboprobe, and the protein identified by the antibody suggesting an mRNA transcytosis process from FCs. At post-vitellogenic stage the CiLgals mainly enrich the GV nucleoplasm, whereas the CinPO2 is contained in TCs and in the ooplasm but never found in the GV. This finding sheds new light on a former paper in which TCs were reported to be the only CinPO2-producing cells in the ovarian follicle. Finally, CiLgals and CinPO2 genes transcription and proteins production seem to be associated with accessory cells during their differentiation from vitellogenic to post-vitellogenic stage. The present findings promote further research on the early upregulation of immune-related genes, and the potential multifunctional role of the produced proteins. In addition further insight on the accessory cells involvement in ascidian oogenesis are reported.

Metatranscriptomic data reveal the effect of different community properties on multifunctional redundancy

The assessment of functional redundancy (FR) is essential to understand community structure-function relationships because FR buffers the functional performance of communities against changes in community composition. We introduce a novel metatranscriptome-based approach to quantify FR, which permits multifunctional aspects to be addressed. FR among prokaryotes was ranked in water samples after exposure to changing salinity. FR was higher for functional categories with mostly broad functions shared among many taxa than for functional categories containing many narrow functions. Furthermore, community characteristics had a higher impact on FR than environmental conditions. The metric also allows FR to be estimated between selected groups of taxa, and FR was high between more closely related organisms if communities were grown in similar environmental conditions. Overall, our data revealed a pronounced influence of functional diversity on the one hand but also the characteristics of individual community members on FR, which was specifically high in those communities whose members were more sensitive to salinity changes.

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams

Understanding microbial communities in terms of taxon and function is essential to decipher the biogeochemical cycling in aquatic ecosystems. Lakes and their input streams are highly linked. However, the differences between microbial assemblages in streams and lakes are still unclear. In this study, we conducted an intensive field sampling of microbial communities from lake water and stream biofilms in the Qinghai Lake watershed, the largest lake in China. We determined bacterial communities using high-throughput 16S rRNA gene sequencing and predicted functional profiles using PICRUSt to determine the taxonomic and functional differences between microbial communities in stream biofilms and lake water. The results showed that stream biofilms and lake water harbored distinct microbial communities. The microbial communities were different taxonomically and functionally between stream and lake. Moreover, streams biofilms had a microbial network with higher connectivity and modularity than lake water. Functional beta diversity was strongly correlated with taxonomic beta diversity in both the stream and lake microbial communities. Lake microbial assemblages displayed greater predicted metabolic potentials of many metabolism pathways while the microbial assemblages in stream biofilms were more abundant in xenobiotic biodegradation and metabolism and lipid metabolism. Furthermore, lake microbial assemblages had stronger predicted metabolic potentials in amino acid metabolism, carbon fixation, and photosynthesis while stream microbial assemblages were higher in carbohydrate metabolism, oxidative phosphorylation, and nitrogen metabolism. This study adds to our knowledge of stream-lake linkages from the functional and taxonomic composition of microbial assemblages.

Biofilm formation and antibiotic susceptibility in dispersed cells versus planktonic cells from clinical, industry and environmental origins

We examined the cell-surface physicochemical properties, the biofilm formation capability and the antibiotic susceptibility in dispersed cells (from an artificial biofilm of alginate beads) and compared with their planktonic (free-swimming) counterparts. The strains used were from different origins, such as clinical (Acinetobacter baumannii AB4), cosmetic industry (Klebsiella oxytoca EU213, Pseudomonas aeruginosa EU190), and environmental (Halomonas venusta MAT28). In general, dispersed cells adhered better to surfaces (measured as the "biofilm index") and had a greater hydrophobicity [measured as the microbial affinity to solvents (MATS)] than planktonic cells. The susceptibility to two antibiotics (ciprofloxacin and tetracycline) of dispersed cells was higher compared with that of their planktonic counterparts (tested by the "bactericidal index"). Dispersed and planktonic cells exhibited differences in cell permeability, especially in efflux pump activity, which could be related to the differences observed in susceptibility to antibiotics. At 1 h of biofilm formation in microtiter plates, dispersed cells treated with therapeutic concentration of ciprofloxacin yielded a lower biofilm index than the control dispersed cells without ciprofloxacin. With respect to the planktonic cells, the biofilm index was similar with and without the ciprofloxacin treatment. In both cases there were a reduction of the number of bacteria measured as viable count of the supernatant. The lower biofilm formation in dispersed cells with ciprofloxacin treatment may be due to a significant increase of biofilm disruption with respect to the biofilm from planktonic cells. From a clinical point of view, biofilms formed on medical devices such as catheters, cells that can be related to an infection were the dispersed cells. Our results showed that early treatment with ciprofloxacin of dispersed cells could diminishe bacterial dispersion and facilitate the partial elimination of the new biofilm formed.

Functional diversity and redundancy across fish gut, sediment and water bacterial communities

This article explores the functional diversity and redundancy in a bacterial metacommunity constituted of three habitats (sediment, water column and fish gut) in a coastal lagoon under anthropogenic pressure. Comprehensive functional gene arrays covering a wide range of ecological processes and stress resistance genes to estimate the functional potential of bacterial communities were used. Then, diversity partitioning was used to characterize functional diversity and redundancy within (α), between (β) and across (γ) habitats. It was showed that all local communities exhibit a highly diversified potential for the realization of key ecological processes and resistance to various environmental conditions, supporting the growing evidence that macro-organisms microbiomes harbour a high functional potential and are integral components of functional gene dynamics in aquatic bacterial metacommunities. Several levels of functional redundancy at different scales of the bacterial metacommunity were observed (within local communities, within habitats and at the metacommunity level). The results suggested a high potential for the realization of spatial ecological insurance within this ecosystem, that is, the functional compensation among microorganisms for the realization and maintenance of key ecological processes, within and across habitats. Finally, the role of macro-organisms as dispersal vectors of microbes and their potential influence on marine metacommunity dynamics were discussed.

Dispersal timing and drought history influence the response of bacterioplankton to drying-rewetting stress

The extent and frequency of drought episodes is expected to increase in the following decades making it a crucial stress factor for smaller water bodies. However, very little is known about how bacterioplankton is affected by increased evaporation and how these communities reassemble after rewetting. Here, we present results from a microcosm experiment that assessed the effect of drying-rewetting stress on bacterioplankton in the light of the stress history and the rate and timing of dispersal after the rewetting. We found that the drying phase resulted mainly in a change of function, whereas the complete desiccation and rewetting processes strongly affected both composition and function, which were, however, influenced by the initial conditions and stress history of the communities. Effects of dispersal were generally stronger when it occurred at an early stage after the rewetting. At this stage, selective establishment of dispersed bacteria coupled with enhanced compositional and functional recovery was found, whereas effects of dispersal were neutral, that is, predictable by dispersal rates, at later stages. Our studies therefore show that both the stress history and the timing of dispersal are important factors that influence the response of bacterial communities to environmental change and stress events.

Do biofilm communities respond to the chemical signatures of fracking? A test involving streams in North-central Arkansas

Background

Unconventional natural gas (UNG) extraction (fracking) is ongoing in 29 North American shale basins (20 states), with ~6000 wells found within the Fayetteville shale (north-central Arkansas). If the chemical signature of fracking is detectable in streams, it can be employed to bookmark potential impacts. We evaluated benthic biofilm community composition as a proxy for stream chemistry so as to segregate anthropogenic signatures in eight Arkansas River catchments. In doing so, we tested the hypothesis that fracking characteristics in study streams are statistically distinguishable from those produced by agriculture or urbanization.

Results

Four tributary catchments had UNG-wells significantly more dense and near to our sampling sites and were grouped as ‘potentially-impacted catchment zones’ (PICZ). Four others were characterized by significantly larger forested area with greater slope and elevation but reduced pasture, and were classified as ‘minimally-impacted’ (MICZ). Overall, 46 bacterial phyla/141 classes were identified, with 24 phyla (52%) and 54 classes (38%) across all samples. PICZ-sites were ecologically more variable than MICZ-sites, with significantly greater nutrient levels (total nitrogen, total phosphorous), and elevated Cyanobacteria as bioindicators that tracked these conditions. PICZ-sites also exhibited elevated conductance (a correlate of increased ion concentration) and depressed salt-intolerant Spartobacteria, suggesting the presence of brine as a fracking effect. Biofilm communities at PICZ-sites were significantly less variable than those at MICZ-sites.

Conclusions

Study streams differed by Group according to morphology, land use, and water chemistry but not in biofilm community structure. Those at PICZ-sites covaried according to anthropogenic impact, and were qualitatively similar to communities found at sites disturbed by fracking. The hypothesis that fracking signatures in study streams are distinguishable from those produced by other anthropogenic effects was statistically rejected. Instead, alterations in biofilm community composition, as induced by fracking, may be less specific than initially predicted, and thus more easily confounded by agriculture and urbanization effects (among others). Study streams must be carefully categorized with regard to the magnitude and extent of anthropogenic impacts. They must also be segregated with statistical confidence (as herein) before fracking impacts are monitored.

Living together in biofilms: the microbial cell factory and its biotechnological implications

In nature, bacteria alternate between two modes of growth: a unicellular life phase, in which the cells are free-swimming (planktonic), and a multicellular life phase, in which the cells are sessile and live in a biofilm, that can be defined as surface-associated microbial heterogeneous structures comprising different populations of microorganisms surrounded by a self-produced matrix that allows their attachment to inert or organic surfaces. While a unicellular life phase allows for bacterial dispersion and the colonization of new environments, biofilms allow sessile cells to live in a coordinated, more permanent manner that favors their proliferation. In this alternating cycle, bacteria accomplish two physiological transitions via differential gene expression: (i) from planktonic cells to sessile cells within a biofilm, and (ii) from sessile to detached, newly planktonic cells. Many of the innate characteristics of biofilm bacteria are of biotechnological interest, such as the synthesis of valuable compounds (e.g., surfactants, ethanol) and the enhancement/processing of certain foods (e.g., table olives). Understanding the ecology of biofilm formation will allow the design of systems that will facilitate making products of interest and improve their yields.

Experimental and Theoretical Investigation of Multispecies Oral Biofilm Resistance to Chlorhexidine Treatment

We investigate recovery of multispecies oral biofilms following chlorhexidine gluconate (CHX) and CHX with surface modifiers (CHX-Plus) treatment. Specifically, we examine the percentage of viable bacteria in the biofilms following their exposure to CHX and CHX-Plus for 1, 3, and 10 minutes, respectively. Before antimicrobial treatment, the biofilms are allowed to grow for three weeks. We find that (a). CHX-Plus kills bacteria in biofilms more effectively than the regular 2% CHX does, (b). cell continues to be killed for up to one week after exposure to the CHX solutions, (c). the biofilms start to recover after two weeks, the percentage of the viable bacteria recovers in the 1 and 3 minutes treatment groups but not in the 10 minutes treatment group after five weeks, and the biofilms fully return to the pretreatment levels after eight weeks. To understand the mechanism, a mathematical model for multiple bacterial phenotypes is developed, adopting the notion that bacterial persisters exist in the biofilms together with regulatory quorum sensing molecules and growth factor proteins. The model reveals the crucial role played by the persisters, quorum sensing molecules, and growth factors in biofilm recovery, accurately predicting the viable bacterial population after CHX treatment.

Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities

Natural communities are open systems and consequently dispersal can play an important role for the diversity, composition and functioning of communities at the local scale. It is, however, still unclear how effects of dispersal differ depending on the initial diversity of local communities. Here we implemented an experiment where we manipulated the initial diversity of natural freshwater bacterioplankton communities using a dilution-to-extinction approach as well as dispersal from a regional species pool. The aim was further to test whether dispersal effects on bacterial abundance and functional parameters (average community growth rates, respiration rates, substrate utilisation ability) differ in dependence of the initial diversity of the communities. First of all, we found that both initial diversity and dispersal rates had an effect on the recruitment of taxa from a regional source, which was higher in communities with low initial diversity and at higher rates of dispersal. Higher initial diversity and dispersal also promoted higher levels of richness and evenness in local communities and affected, both, separately or interactively, the functional performance of communities. Our study therefore suggests that dispersal can influence the diversity, composition and functioning of bacterial communities and that this effect may be enhanced if the initial diversity of communities is depleted.

The complete chloroplast genome sequence of Alocasia macrorrhizos

The complete chloroplast sequence of Alocasia macrorrhizos is 154 995 bp in length, containing a pair of inverted repeats of 25 944 bp separated by a large single-copy (LSC) region and a small single-copy (SSC) region of 87 366 bp and 15 741 bp, respectively. The chloroplast genome encodes 132 predicted functional genes, including 87 protein-coding genes, four ribosomal RNA genes, and 37 transfer RNA genes, 18 of which are duplicated in the inverted repeat regions. In these genes, 16 genes contained single intron and two genes comprising double introns. A maximum-likelihood phylogenetic analysis using complete chloroplast genome revealed that A. macrorrhizos does not belong to Araceae family, which infers that the A. macrorrhizos is distant from the species in Araceae family.

The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation

OBJECTIVES

The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea.

SPATIO-TEMPORAL PATTERNS OF THE MICROBIAL COMMUNITIES

Our results indicated that bacteria (total and β-AOB) showed more spatio-temporal variation than archaea (total and AOA) as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices.

MACROFAUNA, MICROBES AND THE BENTHIC N-CYCLE

Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal activity. We hypothesized that the latter effect can be explained by their bioturbating and bio-irrigating activities, increasing the spatial complexity of the biogeochemical environment.

Coral Mucus Is a Hot Spot for Viral Infections

There is increasing suspicion that viral communities play a pivotal role in maintaining coral health, yet their main ecological traits still remain poorly characterized. In this study, we examined the seasonal distribution and reproduction pathways of viruses inhabiting the mucus of the scleractinians Fungia repanda and Acropora formosa collected in Nha Trang Bay (Vietnam) during an 11-month survey. The strong coupling between epibiotic viral and bacterial abundance suggested that phages are dominant among coral-associated viral communities. Mucosal viruses also exhibited significant differences in their main features between the two coral species and were also remarkably contrasted with their planktonic counterparts. For example, their abundance (inferred from epifluorescence counts), lytic production rates (KCN incubations), and the proportion of lysogenic cells (mitomycin C inductions) were, respectively, 2.6-, 9.5-, and 2.2-fold higher in mucus than in the surrounding water. Both lytic and lysogenic indicators were tightly coupled with temperature and salinity, suggesting that the life strategy of viral epibionts is strongly dependent upon environmental circumstances. Finally, our results suggest that coral mucus may represent a highly favorable habitat for viral proliferation, promoting the development of both temperate and virulent phages. Here, we discuss how such an optimized viral arsenal could be crucial for coral viability by presumably forging complex links with both symbiotic and adjacent nonsymbiotic microorganisms.

Biodiversity, community structure and function of biofilms in stream ecosystems

Multi-species, surface-attached biofilms often dominate microbial life in streams and rivers, where they contribute substantially to biogeochemical processes. The microbial diversity of natural biofilms is huge, and may have important implications for the functioning of aquatic environments and the ecosystem services they provide. Yet the causes and consequences of biofilm biodiversity remain insufficiently understood. This review aims to give an overview of current knowledge on the distribution of stream biofilm biodiversity, the mechanisms generating biodiversity patterns and the relationship between biofilm biodiversity and ecosystem functioning.

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.

Biodiversity enhances ecosystem multifunctionality across trophic levels and habitats

The importance of biodiversity for the integrated functioning of ecosystems remains unclear because most evidence comes from analyses of biodiversity's effect on individual functions. Here we show that the effects of biodiversity on ecosystem function become more important as more functions are considered. We present the first systematic investigation of biodiversity's effect on ecosystem multifunctionality across multiple taxa, trophic levels and habitats using a comprehensive database of 94 manipulations of species richness. We show that species-rich communities maintained multiple functions at higher levels than depauperate ones. These effects were stronger for herbivore biodiversity than for plant biodiversity, and were remarkably consistent across aquatic and terrestrial habitats. Despite observed tradeoffs, the overall effect of biodiversity on multifunctionality grew stronger as more functions were considered. These results indicate that prior research has underestimated the importance of biodiversity for ecosystem functioning by focusing on individual functions and taxonomic groups.

The influence of biodiversity on multiple ecosystem processes is not well understood. Analysing 94 biodiversity-ecosystem functioning experiments, Lefcheck et al. find that increased species richness maintains more ecological functions, across multiple taxa, trophic levels and habitats.

Bacterial community analysis of drinking water biofilms in southern Sweden

Next-generation sequencing of the V1-V2 and V3 variable regions of the 16S rRNA gene generated a total of 674,116 reads that described six distinct bacterial biofilm communities from both water meters and pipes. A high degree of reproducibility was demonstrated for the experimental and analytical work-flow by analyzing the communities present in parallel water meters, the rare occurrence of biological replicates within a working drinking water distribution system. The communities observed in water meters from households that did not complain about their drinking water were defined by sequences representing Proteobacteria (82-87%), with 22-40% of all sequences being classified as Sphingomonadaceae. However, a water meter biofilm community from a household with consumer reports of red water and flowing water containing elevated levels of iron and manganese had fewer sequences representing Proteobacteria (44%); only 0.6% of all sequences were classified as Sphingomonadaceae; and, in contrast to the other water meter communities, markedly more sequences represented Nitrospira and Pedomicrobium. The biofilm communities in pipes were distinct from those in water meters, and contained sequences that were identified as Mycobacterium, Nocardia, Desulfovibrio, and Sulfuricurvum. The approach employed in the present study resolved the bacterial diversity present in these biofilm communities as well as the differences that occurred in biofilms within a single distribution system, and suggests that next-generation sequencing of 16S rRNA amplicons can show changes in bacterial biofilm communities associated with different water qualities.

Higher biodiversity is required to sustain multiple ecosystem processes across temperature regimes

Biodiversity loss is occurring rapidly worldwide, yet it is uncertain whether few or many species are required to sustain ecosystem functioning in the face of environmental change. The importance of biodiversity might be enhanced when multiple ecosystem processes (termed multifunctionality) and environmental contexts are considered, yet no studies have quantified this explicitly to date. We measured five key processes and their combined multifunctionality at three temperatures (5, 10 and 15 °C) in freshwater aquaria containing different animal assemblages (1-4 benthic macroinvertebrate species). For single processes, biodiversity effects were weak and were best predicted by additive-based models, i.e. polyculture performances represented the sum of their monoculture parts. There were, however, significant effects of biodiversity on multifunctionality at the low and the high (but not the intermediate) temperature. Variation in the contribution of species to processes across temperatures meant that greater biodiversity was required to sustain multifunctionality across different temperatures than was the case for single processes. This suggests that previous studies might have underestimated the importance of biodiversity in sustaining ecosystem functioning in a changing environment.

Relationships between bacterial community composition, functional trait composition and functioning are context dependent--but what is the context?

Bacterial communities are immensely diverse and drive many fundamental ecosystem processes. However, the role of bacterial community composition (BCC) for functioning is still unclear. Here we evaluate the relative importance of BCC (from 454-sequencing), functional traits (from Biolog Ecoplates) and environmental conditions for per cell biomass production (BPC; ³H-leucine incorporation) in six data sets of natural freshwater bacterial communities. BCC explained significant variation of BPC in all six data sets and most variation in four. BCC measures based on 16S rRNA (active bacteria) did not consistently explain more variation in BPC than measures based on the 16S rRNA-gene (total community), and adding phylogenetic information did not, in general, increase the explanatory power of BCC. In contrast to our hypothesis, the importance of BCC for BPC was not related to the anticipated dispersal rates in and out of communities. Functional traits, most notably the ability to use cyclic and aromatic compounds, as well as local environmental conditions, i.e. stoichiometric relationships of nutrients, explained some variation in all six data sets. In general there were weak associations between variation in BCC and variation in the functional traits contributing to productivity. This indicates that additional traits may be important for productivity as well. By comparing several data sets obtained in a similar way we conclude that no single measure of BCC was obviously better than another in explaining BPC. We identified some key functional traits for productivity, but although there was a coupling between BCC, functional traits and productivity, the strength of the coupling seems context dependent. However, the exact context is still unresolved.

Effects of warming on stream biofilm organic matter use capabilities

The understanding of ecosystem responses to changing environmental conditions is becoming increasingly relevant in the context of global warming. Microbial biofilm communities in streams play a key role in organic matter cycling which might be modulated by shifts in flowing water temperature. In this study, we performed an experiment at the Candal stream (Portugal) longitudinally divided into two reaches: a control half and an experimental half where water temperature was 3 °C above that of the basal stream water. Biofilm colonization was monitored during 42 days in the two stream halves. Changes in biofilm function (extracellular enzyme activities and carbon substrate utilization profiles) as well as chlorophyll a and prokaryote densities were analyzed. The biofilm in the experimental half showed a higher capacity to decompose cellulose, hemicellulose, lignin, and peptidic compounds. Total leucine-aminopeptidase, cellobiohydrolase and β-xylosidase showed a respective 93, 66, and 61% increase in activity over the control; much higher than would be predicted by only the direct temperature physical effect. In contrast, phosphatase and lipase activity showed the lowest sensitivity to temperature. The biofilms from the experimental half also showed a distinct functional fingerprint and higher carbon usage diversity and richness, especially due to a wider use of polymers and carbohydrates. The changes in the biofilm functional capabilities might be indirectly affected by the higher prokaryote and chlorophyll density measured in the biofilm of the experimental half. The present study provides evidence that a realistic stream temperature increase by 3 °C changes the biofilm metabolism to a greater decomposition of polymeric complex compounds and peptides but lower decomposition of lipids. This might affect stream organic matter cycling and the transfer of carbon to higher trophic levels.