A Mini-review of Microbial Consortia: Their Roles in Aquatic Production and Biogeochemical Cycling

Adaption and application of cell-based bioassays to whole-water samples

The increasing presence of contaminants of emerging concern in wastewater and their potential environmental risks require improved monitoring and analysis methods. Direct toxicity assessment (DTA) using bioassays can complement chemical analysis of wastewater discharge, but traditional in vivo tests have ethical considerations and are expensive, low-throughput, and limited to apical endpoints (mortality, reproduction, development, and growth). In vitro bioassays offer an alternative approach that is cheaper, faster, and more ethical, and can provide higher sensitivity for some environmentally relevant endpoints. This study explores the potential benefits of using whole water samples of wastewater and environmental surface water instead of traditional solid phase extraction (SPE) methods for in vitro bioassays testing. Whole water samples produced a stronger response in most bioassays, likely due to the loss or alteration of contaminants during SPE sample extraction. In addition, there was no notable difference in results for most bioassays after freezing whole water samples, which allows for increased flexibility in testing timelines and cost savings. These findings highlight the potential advantages of using whole water samples in DTA and provide a framework for future research in this area.

Exploring the prokaryote-eukaryote interplay in microbial mats from an Andean athalassohaline wetland

Microbial community assembly results from the interaction between biotic and abiotic factors. However, environmental selection is thought to predominantly shape communities in extreme ecosystems. Salar de Huasco, situated in the high-altitude Andean Altiplano, represents a poly-extreme ecosystem displaying spatial gradients of physicochemical conditions. To disentangle the influence of abiotic and biotic factors, we studied prokaryotic and eukaryotic communities from microbial mats and underlying sediments across contrasting areas of this athalassohaline ecosystem. The prokaryotic communities were primarily composed of bacteria, notably including a significant proportion of photosynthetic organisms like Cyanobacteria and anoxygenic photosynthetic members of Alpha- and Gammaproteobacteria and Chloroflexi. Additionally, Bacteroidetes, Verrucomicrobia, and Deltaproteobacteria were abundantly represented. Among eukaryotes, photosynthetic organisms (Ochrophyta and Archaeplastida) were predominant, alongside relatively abundant ciliates, cercozoans, and flagellated fungi. Salinity emerged as a key driver for the assembly of prokaryotic communities. Collectively, abiotic factors influenced both prokaryotic and eukaryotic communities, particularly those of algae. However, prokaryotic communities strongly correlated with photosynthetic eukaryotes, suggesting a pivotal role of biotic interactions in shaping these communities. Co-occurrence networks suggested potential interactions between different organisms, such as diatoms with specific photosynthetic and heterotrophic bacteria or with protist predators, indicating influences beyond environmental selection. While some associations may be explained by environmental preferences, the robust biotic correlations, alongside insights from other ecosystems and experimental studies, suggest that symbiotic and trophic interactions significantly shape microbial mat and sediment microbial communities in this athalassohaline ecosystem.IMPORTANCEHow biotic and abiotic factors influence microbial community assembly is still poorly defined. Here, we explore their influence on prokaryotic and eukaryotic community assembly within microbial mats and sediments of an Andean high-altitude polyextreme wetland system. We show that, in addition to abiotic elements, mutual interactions exist between prokaryotic and eukaryotic communities. Notably, photosynthetic eukaryotes exhibit a strong correlation with prokaryotic communities, specifically diatoms with certain bacteria and other protists. Our findings underscore the significance of biotic interactions in community assembly and emphasize the necessity of considering the complete microbial community.

Antiviral discovery in toxic cyanobacteria: Low hanging fruit in the age of pandemics

The power of novel vaccination technologies and their rapid development were elucidated clearly during the COVID-19 pandemic. At the same time, it also became clear that there is an urgent need to discover and manufacture new antivirals that target emerging viral threats. Toxic species of cyanobacteria produce a range of bioactive compounds that makes them good candidates for drug discovery. Nevertheless, few studies demonstrate the antiviral potential of cyanobacteria. This is partly due to the lack of specific and simple protocols designed for the rapid detection of antiviral activity in cyanobacteria and partly because specialized facilities for work with pathogenic viruses are few and far between. We therefore developed an easy method for the screening of cyanobacterial cultures for antiviral activity and used our private culture collection of non-pathogenic virus isolates to show that antiviral activity is a prominent feature in the cyanobacterium Microcystis aeruginosa. In this proof-of-concept study, we show that M. aeruginosa extracts from three different cyanobacterial strains delay infection of diatom-infecting single-stranded DNA and single-stranded RNA viruses by up to 2 days. Our work shows the ease with which cyanobacteria from culture collections can be screened for antiviral activity and highlights the potential of cyanobacteria as an excellent source for the discovery of novel antiviral compounds, warranting further investigation.

Elimination of inhibitory effects of dodecyl dimethyl benzyl ammonium chloride on microalgae in wastewater by cocultivation with a newly screened microbial consortium

As one of the most commonly used biocidal cationic surfactants, benzalkonium chlorides (BACs) have been an increasing concern as emerging contaminants. Wastewater has been claimed the main point for BACs to enter into the environment, but to date, it is still largely unknown how the BACs affect the microbes (especially microalgae) in the practical wastewater and how to cost-effectively remove them. In this study, the inhibitory effects of a typical BACs, dodecyl dimethyl benzyl ammonium chloride (DDBAC), on a green microalga Chlorella sp. in oxidation pond wastewater were investigated. The results showed that though a hermetic effect at the first 2 days was observed with the DDBAC at low concentration (<6 mg/L), the algal growth and photosynthesis were significantly inhibited by the DDBAC at all the tested concentrations (3 to 48 mg/L). Fortunately, a new microbial consortium (MC) capable of degrading DDBAC was screened through a gradient domestication method. The MC mainly composed of Wickerhamomyces sp., Purpureocillium sp., and Achromobacter sp., and its maximum removal efficiency and removal rate of DDBAC (48 mg/L) respectively reached 98.1 % and 46.32 mg/L/d. Interestingly, a microbial-microalgal system (MMS) was constructed using the MC and Chlorella sp., and a synergetic effect between the two kinds of microorganisms was proposed: microalga provided oxygen and extracellular polysaccharides as co-metabolic substrates to help the MC to degrade DDBAC, while the MC helped to eliminate the DDBAC-induced inhibition on the alga. Further, by observing the seven kinds of degradation products (mainly including CH5O3P, C6H5CH2-, and C8H11N), two possible chemical pathways of the DDBAC degradation were proposed. In addition, the metagenomic sequencing results showed that the main functional genes of the MMS included antibiotic-resistant genes, ABC transporter genes, quorum sensing genes, two-component regulatory system genes, etc. This study provided some theoretical and application findings for the cost-effective pollution prevention of BACs in wastewater.

Pairing metagenomics and metaproteomics to characterize ecological niches and metabolic essentiality of gut microbiomes

The genome of a microorganism encodes its potential functions that can be implemented through expressed proteins. It remains elusive how a protein's selective expression depends on its metabolic essentiality to microbial growth or its ability to claim resources as ecological niches. To reveal a protein's metabolic or ecological role, we developed a computational pipeline, which pairs metagenomics and metaproteomics data to quantify each protein's gene-level and protein-level functional redundancy simultaneously. We first illustrated the idea behind the pipeline using simulated data of a consumer-resource model. We then validated it using real data from human and mouse gut microbiome samples. In particular, we analyzed ABC-type transporters and ribosomal proteins, confirming that the metabolic and ecological roles predicted by our pipeline agree well with prior knowledge. Finally, we performed in vitro cultures of a human gut microbiome sample and investigated how oversupplying various sugars involved in ecological niches influences the community structure and protein abundance. The presented results demonstrate the performance of our pipeline in identifying proteins' metabolic and ecological roles, as well as its potential to help us design nutrient interventions to modulate the human microbiome.

Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes

Microbiome engineering offers the potential to leverage microbial communities to improve outcomes in human health, agriculture, and climate. To translate this potential into reality, it is crucial to reliably predict community composition and function. But a brute force approach to cataloging community function is hindered by the combinatorial explosion in the number of ways we can combine microbial species. An alternative is to parameterize microbial community outcomes using simplified, mechanistic models, and then extrapolate these models beyond where we have sampled. But these approaches remain data-hungry, as well as requiring an a priori specification of what kinds of mechanisms are included and which are omitted. Here, we resolve both issues by introducing a mechanism-agnostic approach to predicting microbial community compositions and functions using limited data. The critical step is the identification of a sparse representation of the community landscape. We then leverage this sparsity to predict community compositions and functions, drawing from techniques in compressive sensing. We validate this approach on in silico community data, generated from a theoretical model. By sampling just [Formula: see text]1% of all possible communities, we accurately predict community compositions out of sample. We then demonstrate the real-world application of our approach by applying it to four experimental datasets and showing that we can recover interpretable, accurate predictions on composition and community function from highly limited data.

New insight into the mechanisms of autochthonous fungal bioaugmentation of phenanthrene in petroleum contaminated soil by stable isotope probing

Autochthonous fungal bioaugmentation (AFB) is considered a reliable bioremediation approach for polycyclic aromatic hydrocarbon (PAH) contamination, but little is known about its mechanisms in contaminated soils. Here, a microcosm experiment was performed to explore the AFB mechanisms associated with two highly efficient phenanthrene degrading agents of fungi (with laccase-producing Scedosporium aurantiacum GIG-3 and non-laccase-producing Aspergillus fumigatus LJD-29), using stable-isotope-probing (SIP) and high-throughput sequencing. The results showed that each fungus markedly improved phenanthrene removal, and microcosms with both fungi exhibited the best phenanthrene removal performance among all microcosms. Additionally, AFB markedly shifted the composition of the microbial community, particularly the phenanthrene-degrading bacterial taxa. Interestingly, based on SIP results, strains GIG-3 and LJD-29 did not assimilate phenanthrene directly during AFB, but instead played key roles in the preliminary decomposition of phenanthrene though secretion of different extracellular enzymes to oxidize the benzene ring (GIG-3 bioaugmentation with laccase, and LJD-29 bioaugmentation with manganese and lignin peroxidases). In addition, all functional degraders directly involved in phenanthrene assimilation were indigenous bacteria, while native fungi rarely participated in the direct phenanthrene mineralization. Our findings provide a new mechanism of AFB with multiple fungi, and support AFB as a promising strategy for the in situ bioremediation of PAH-contaminated soil.

Climate change and the aquatic continuum: A cyanobacterial comeback story

Billions of years ago, the Earth's waters were dominated by cyanobacteria. These microbes amassed to such formidable numbers, they ushered in a new era-starting with the Great Oxidation Event-fuelled by oxygenic photosynthesis. Throughout the following eon, cyanobacteria ceded portions of their global aerobic power to new photoautotrophs with the rise of eukaryotes (i.e. algae and higher plants), which co-existed with cyanobacteria in aquatic ecosystems. Yet while cyanobacteria's ecological success story is one of the most notorious within our planet's biogeochemical history, scientists to this day still seek to unlock the secrets of their triumph. Now, the Anthropocene has ushered in a new era fuelled by excessive nutrient inputs and greenhouse gas emissions, which are again reshaping the Earth's biomes. In response, we are experiencing an increase in global cyanobacterial bloom distribution, duration, and frequency, leading to unbalanced, and in many instances degraded, ecosystems. A critical component of the cyanobacterial resurgence is the freshwater-marine continuum: which serves to transport blooms, and the toxins they produce, on the premise that "water flows downhill". Here, we identify drivers contributing to the cyanobacterial comeback and discuss future implications in the context of environmental and human health along the aquatic continuum. This Minireview addresses the overlooked problem of the freshwater to marine continuum and the effects of nutrients and toxic cyanobacterial blooms moving along these waters. Marine and freshwater research have historically been conducted in isolation and independently of one another. Yet, this approach fails to account for the interchangeable transit of nutrients and biology through and between these freshwater and marine systems, a phenomenon that is becoming a major problem around the globe. This Minireview highlights what we know and the challenges that lie ahead.

Phosphorus Accumulation in Extracellular Polymeric Substances (EPS) of Colony-Forming Cyanobacteria Challenges Imbalanced Nutrient Reduction Strategies in Eutrophic Lakes

Extracellular polymeric substances (EPS) are crucial for cyanobacterial proliferation; however, certain queries, including how EPS affects cellular nutrient processes and what are the implications for nutrient management in lakes, are not well documented. Here, the dynamics of cyanobacterial EPS-associated phosphorus (EPS-P) were examined both in a shallow eutrophic lake (Lake Taihu, China) and in laboratory experiments with respect to nitrogen (N) and phosphorus (P) availability. Results indicated that 40-65% of the total cyanobacterial aggregate/particulate P presented as EPS-P (mainly labile P and Fe/Al-P). Phosphorus-starved cyanobacteria rapidly replenished their EPS-P pools after the P was resupplied, and the P concentration in this pool was stable for long afterward, although the environmental P concentration decreased dramatically. A low-N treatment enhanced the EPS production alongside two-fold EPS-P accumulation (particularly labile P) higher than the control. Such patterns occurred in the lake where EPS and EPS-P contents were high under N limitation. EPS-P enrichment increased the P content in cyanobacteria; subsequently, it could hold the total P concentration higher for longer and make bloom mitigation harder. The findings outline a new insight into EPS functions in the P process of cyanobacterial aggregates and encourage consideration of both N and P reductions in nutrient management.

Ecological landscapes guide the assembly of optimal microbial communities

Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with the number of species, and so an exhaustive search cannot be performed even for a dozen species. A heuristic search that improves community function by adding or removing one species at a time is more practical, but it is unknown whether this strategy can discover an optimal or nearly optimal community. Using consumer-resource models with and without cross-feeding, we investigate how the efficacy of search depends on the distribution of resources, niche overlap, cross-feeding, and other aspects of community ecology. We show that search efficacy is determined by the ruggedness of the appropriately-defined ecological landscape. We identify specific ruggedness measures that are both predictive of search performance and robust to noise and low sampling density. The feasibility of our approach is demonstrated using experimental data from a soil microbial community. Overall, our results establish the conditions necessary for the success of the heuristic search and provide concrete design principles for building high-performing microbial consortia.

Mechanisms driving spatial distribution of residents in colony biofilms: an interdisciplinary perspective

Biofilms are consortia of microorganisms that form collectives through the excretion of extracellular matrix compounds. The importance of biofilms in biological, industrial and medical settings has long been recognized due to their emergent properties and impact on surrounding environments. In laboratory situations, one commonly used approach to study biofilm formation mechanisms is the colony biofilm assay, in which cell communities grow on solid-gas interfaces on agar plates after the deposition of a population of founder cells. The residents of a colony biofilm can self-organize to form intricate spatial distributions. The assay is ideally suited to coupling with mathematical modelling due to the ability to extract a wide range of metrics. In this review, we highlight how interdisciplinary approaches have provided deep insights into mechanisms causing the emergence of these spatial distributions from well-mixed inocula.

Cross-feeding between cyanobacterium Synechococcus and Escherichia coli in an artificial autotrophic–heterotrophic coculture system revealed by integrated omics analysis

Background

Light-driven consortia, which consist of sucrose-secreting cyanobacteria and heterotrophic species, have attracted considerable attention due to their capability for the sustainable production of valuable chemicals directly from CO₂. In a previous study, we achieved a one-step conversion of sucrose secreted from cyanobacteria to fine chemicals by constructing an artificial coculture system consisting of sucrose-secreting Synechococcus elongateus cscB⁺ and 3-hydroxypropionic acid (3-HP) producing Escherichia coli ABKm. Analyses of the coculture system showed that the cyanobacterial cells grew better than their corresponding axenic cultures. To explore the underlying mechanism and to identify the metabolic nodes with the potential to further improve the coculture system, we conducted integrated transcriptomic, proteomic and metabolomic analyses.

Results

We first explored how the relieved oxidative stress affected cyanobacterial cell growth in a coculture system by supplementing additional ascorbic acid to CoBG-11 medium. We found that the cell growth of cyanobacteria was clearly improved with an additional 1 mM ascorbic acid under axenic culture; however, its growth was still slower than that in the coculture system, suggesting that the improved growth of Synechococcus cscB⁺ may be caused by multiple factors, including reduced oxidative stress. To further explore the cellular responses of cyanobacteria in the system, quantitative transcriptomics, proteomics and metabolomics were applied to Synechococcus cscB⁺. Analyses of differentially regulated genes/proteins and the abundance change of metabolites in the photosystems revealed that the photosynthesis of the cocultured Synechococcus cscB⁺ was enhanced. The decreased expression of the CO₂ transporter suggested that the heterotrophic partner in the system might supplement additional CO₂ to support the cell growth of Synechococcus cscB⁺. In addition, the differentially regulated genes and proteins involved in the nitrogen and phosphate assimilation pathways suggested that the supply of phosphate and nitrogen in the Co-BG11 medium might be insufficient.

Conclusion

An artificial coculture system capable of converting CO₂ to fine chemicals was established and then analysed by integrated omics analysis, which demonstrated that in the coculture system, the relieved oxidative stress and increased CO₂ availability improved the cell growth of cyanobacteria. In addition, the results also showed that the supply of phosphate and nitrogen in the Co-BG11 medium might be insufficient, which paves a new path towards the optimization of the coculture system in the future. Taken together, these results from the multiple omics analyses provide strong evidence that beneficial interactions can be achieved from cross-feeding and competition between phototrophs and prokaryotic heterotrophs and new guidelines for engineering more intelligent artificial consortia in the future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13068-022-02163-5.

Environmental and Biological Controls on Sedimentary Bottom Types in the Puquios of the Salar de Llamara, Northern Chile

The Puquios of the Salar de Llamara in the Atacama Desert, northern Chile, is a system of small lakes that is characterized by evaporitic mineral deposition and that commonly hosts microbial communities. This region is known for its extreme aridity, solar irradiance, and temperature fluctuations. The Puquios are a highly diverse ecosystem with a variety of sedimentary bottom types. Our previous results identified electrical conductivity (EC) as a first-order environmental control on bottom types. In the present paper, we extend our analysis to examine the effects of additional environmental parameters on bottom types and to consider reasons for the importance of EC as a control of sedimentology. Our results identify microbially produced extracellular polymeric substances (EPS) as a major player in the determination of bottom types. The relative amounts and properties of EPS are determined by EC. EPS, in turn, determines the consistency of bottom types, exchange of bottom substrate with the overlying water column, and mineral precipitation within the substrate. Low-EC ponds in the Puquios system have flocculent to semi-cohesive bottom types, with low-viscosity EPS that allows for high-exchange with the surrounding waters and mineral precipitation of granular gypsum, carbonate, and Mg–Si clay in close association with microbes. Ponds with elevated EC have bottom types that are laminated and highly cohesive with high-viscosity EPS that restricts the exchange between sediments and the surrounding waters; mineral precipitation in these high-EC ponds includes granular to laminated gypsum, carbonate and Mg–Si, which also form in close association with microbes. Bottom types in ponds with EC above the threshold for thriving benthic microbial communities have insufficient EPS accumulations to affect mineral precipitation, and the dominant mineral is gypsum (selenite). The variations in EPS production throughout the Puquios, associated with heterogeneity in environmental conditions, make the Puquios region an ideal location for understanding the controls of sedimentary bottom types in evaporative extreme environments that may be similar to those that existed on early Earth and beyond.

Dynamic Phycobilin Pigment Variations in Diazotrophic and Non-diazotrophic Cyanobacteria Batch Cultures Under Different Initial Nitrogen Concentrations

Increased anthropogenic nutrient loading has led to eutrophication of aquatic ecosystems, which is the major cause of harmful cyanobacteria blooms. Element stoichiometry of cyanobacteria bloom is subject to nutrient availabilities and may significantly contribute to primary production and biogeochemical cycling. Phycobilisome is the antenna of the photosynthetic pigment apparatus in cyanobacteria, which contains phycobilin pigments (PBPs) and linker proteins. This nitrogen (N)-rich protein complex has the potential to support growth as a N-storage site and may play a major role in the variability of cyanobacteria N stoichiometry. However, the regulation of PBPs during bloom formation remains unclear. We investigated the temporal variation of N allocation into PBPs and element stoichiometry for two ubiquitous cyanobacteria species, Microcystis aeruginosa and Dolichospermum flos-aquae, in a batch culture experiment with different initial N availabilities. Our results indicated that the N allocation into PBPs is species-dependent and tightly regulated by the availability of nutrients fueling population expansion. During the batch culture experiment, different nutrient uptake rates led to distinct stoichiometric imbalances of N and phosphorus (P), which substantially altered cyanobacteria C: N and C: P stoichiometry. Microcystis invested cellular N into PBPs and exhibited greater flexibility in C: N and C: P stoichiometry than D. flos-aquae. The dynamics of such N-rich macromolecules may help explain the N stoichiometry variation during a bloom and the interspecific difference between M. aeruginosa and D. flos-aquae. Our study provides a quantitative understanding of the elemental stoichiometry and the regulation of PBPs for non-diazotrophic and diazotrophic cyanobacteria blooms.

Founder cell configuration drives competitive outcome within colony biofilms

Bacteria can form dense communities called biofilms, where cells are embedded in a self-produced extracellular matrix. Exploiting competitive interactions between strains within the biofilm context can have potential applications in biological, medical, and industrial systems. By combining mathematical modelling with experimental assays, we reveal that spatial structure and competitive dynamics within biofilms are significantly affected by the location and density of the founder cells used to inoculate the biofilm. Using a species-independent theoretical framework describing colony biofilm formation, we show that the observed spatial structure and relative strain biomass in a mature biofilm comprising two isogenic strains can be mapped directly to the geographical distributions of founder cells. Moreover, we define a predictor of competitive outcome that accurately forecasts relative abundance of strains based solely on the founder cells’ potential for radial expansion. Consequently, we reveal that variability of competitive outcome in biofilms inoculated at low founder density is a natural consequence of the random positioning of founding cells in the inoculum. Extension of our study to non-isogenic strains that interact through local antagonisms, shows that even for strains with different competition strengths, a race for space remains the dominant mode of competition in low founder density biofilms. Our results, verified by experimental assays using Bacillus subtilis, highlight the importance of spatial dynamics on competitive interactions within biofilms and hence to related applications.

Fire as a driver of fungal diversity - A synthesis of current knowledge

Fires occur in most terrestrial ecosystems where they drive changes in the traits, composition, and diversity of fungal communities. Fires range from rare, stand-replacing wildfires to frequent, prescribed fires used to mimic natural fire regimes. Fire regime factors, including burn severity, fire intensity, and timing, vary widely and likely determine how fungi respond to fires. Despite the importance of fungi to post-fire plant communities and ecosystem functioning, attempts to identify common fungal responses and their major drivers are lacking. This synthesis addresses this knowledge gap and ranges from fire adaptations of specific fungi to succession and assembly fungal communities as they respond to spatially heterogenous burning within the landscape. Fires impact fungi directly and indirectly through their effects on fungal survival, substrate and habitat modifications, changes in environmental conditions, and/or physiological responses of the hosts with which fungi interact. Some specific pyrophilous, or "fire-loving," fungi often appear after fire. Our synthesis explores whether such taxa can be considered cosmopolitan, and whether they are truly fire-adapted or simply opportunists adapted to rapidly occupy substrates and habitats made available by fires. We also discuss the possible inoculum sources of post-fire fungi and explore existing conceptual models and ecological frameworks that may be useful in generalizing fungal fire responses. We conclude with identifying research gaps and areas that may best transform the current knowledge and understanding of fungal responses to fire.

Soil microbial co-occurrence networks become less connected with soil development in a high Arctic glacier foreland succession

Classically, ecologists have considered that biota becomes more integrated and interdependent with ecosystem development in primary successional environments. However, recent work on soil microbial communities suggests that there may in fact be no change in network integration over successional time series. Here, we performed a test of this principle by identifying network-level topological features of the soil microbial co-occurrence networks in the primary successional foreland environment of the retreating high-Arctic glacier of Midtre Lovénbreen, Svalbard. Soil was sampled at sites along the foreland of inferred ages 10-90 years since deglaciation. DNA was extracted and amplicon sequenced for 16 s rRNA genes for bacteria and ITS1 region for fungi. Despite the chronologically-related soil pH decline and organic C/N accumulation, analysis on network-level topological features showed network integration did not change with inferred chronological ages, whereas network integration declined with decreasing pH and increasing total organic carbon (TOC) - both factors that can be viewed as an indicator of soil development. We also found that bacteria played a greater role in the network structure than fungi, with all keystone species in the microbial co-occurrence network being bacteria species. Both number and relative abundance of the keystone species were significantly higher when soil pH increased or TOC decreased. It appears that in the more extreme and less productive conditions of early primary succession, integration between members of soil biota into consortia may play a greater role in niche adaptation and survival. Our finding also emphasizes that ecosystem development is not simply a product of time but is influenced by locally heterogeneous factors.

The Dark Side of Microbial Processes: Accumulation of Nitrate During Storage of Surface Water in the Dark and the Underlying Mechanism

In densely populated cities with limited land, storage of surface water in underground spaces is a potential solution to meet the rising demand of clean water. In addition, due to the imperative need of renewable solar energy and limited land resources, the deployment of floating solar photovoltaic (PV) systems over water has risen exponentially. In both scenarios, microbial communities in the water do not have access to sunlight. How the absence of sunlight influences microbial community function and the water quality is largely unknown. The objective of this study was to reveal microbial processes in surface water stored in the dark and water quality dynamics. Water from a freshwater reservoir was stored in the dark or light (control) for 6 months. Water quality was monitored at regular intervals. RNA sequencing was performed on the Illumina MiSeq platform and qPCR was used to substantiate the findings arising from the sequencing data. Our results showed that storage of surface water in the dark resulted in the accumulation of nitrate in the water. Storage in the dark promoted the decay of algal cells, increasing the amount of free nitrogen in the water. Most of the free nitrogen was eventually transformed into nitrate through microbial processes. RNA sequencing-based microbial community analyses and pure culture experiments using nitrifying bacteria Nitrosomonas europaea and Nitrobacter sp. revealed that the accumulation of nitrate in the dark was likely due to an increase in nitrification rate and a decrease in the assimilation rate of nitrate back into the biomass. IMPORTANCE Microbial communities play an essential role in maintaining a healthy aquatic ecosystem. For example, in surface water reservoirs, microorganisms produce oxygen, break down toxic contaminants and remove excess nitrogen. In densely populated cities with limited land, storing surface water in underground spaces and deploying floating solar photovoltaic (PV) systems over water are potential solutions to address water and energy sustainability challenges. In both scenarios, surface water is kept in the dark. In this work, we revealed how the absence of sunlight influences microbial community function and water quality. We showed that storage of surface water in the dark affected bacterial activities responsible for nitrogen transformation, resulting in the accumulation of nitrate in the water. Our findings highlight the importance of monitoring nitrate closely if raw surface water is to be stored in the dark and the potential need of downstream treatment to remove nitrate.

Conceptual strategies for characterizing interactions in microbial communities

Understanding the sets of inter- and intraspecies interactions in microbial communities is a fundamental goal of microbial ecology. However, the study and quantification of microbial interactions pose several challenges owing to their complexity, dynamic nature, and the sheer number of unique interactions within a typical community. To overcome such challenges, microbial ecologists must rely on various approaches to distill the system of study to a functional and conceptualizable level, allowing for a practical understanding of microbial interactions in both simplified and complex systems. This review broadly addresses the role of several conceptual approaches available for the microbial ecologist’s arsenal, examines specific tools used to accomplish such approaches, and describes how the assumptions, expectations, and philosophies underlying these tools change across scales of complexity.

Ecological Interactions of Cyanobacteria and Heterotrophs Enhances the Robustness of Cyanobacterial Consortium for Carbon Sequestration

Lack of robustness is a major barrier to foster a sustainable cyanobacterial biotechnology. Use of cyanobacterial consortium increases biodiversity, which provides functional redundancy and prevents invading species from disrupting the production ecosystem. Here we characterized a cyanobacterial consortium enriched from microbial mats of alkaline soda lakes in BC, Canada, at high pH and alkalinity. This consortium has been grown in open laboratory culture for 4 years without crashes. Using shotgun metagenomic sequencing, 29 heterotrophic metagenome-assembled-genomes (MAGs) were retrieved and were assigned to Bacteroidota, Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobiota, Patescibacteria, Planctomycetota, and Archaea. In combination with metaproteomics, the overall stability of the consortium was determined under different cultivation conditions. Genome information from each heterotrophic population was investigated for six ecological niches created by cyanobacterial metabolism and one niche for phototrophy. Genome-resolved metaproteomics with stable isotope probing using 13C-bicarbonate (protein/SIP) showed tight coupling of carbon transfer from cyanobacteria to the heterotrophic populations, specially Wenzhouxiangella. The community structure was compared to a previously described consortium of a closely related cyanobacteria, which indicated that the results may be generalized. Productivity losses associated with heterotrophic metabolism were relatively small compared to other losses during photosynthesis.

Mutualistic relationship between Nitrospira and concomitant heterotrophs

Nitrifying chemoautotrophs support the growth of diverse concomitant heterotrophs in natural or engineered environments by supplying organic compounds. In this study, we aimed to investigate this microbial association, especially (i) to distinguish whether the relationship between nitrifying chemoautotrophs and heterotrophs is commensal or mutualistic, and (ii) to clarify how heterotrophs promote the growth of autotrophic nitrite-oxidizing bacteria (Nitrospira). Pure cultured Nitrospira (Nitrospira sp. ND1) was employed in this study. Heterotrophs growing with metabolic by-products of Nitrospira as a sole carbon source were isolated from several environmental samples and used to test the growth-promoting activity of Nitrospira. Furthermore, liquid chromatography-mass spectrometry analysis was conducted to evaluate how heterotrophs consumed chemical compounds produced by Nitrospira and newly produced during co-cultivation. Notably, Nitrospira growth was stimulated by co-cultivation with some heterotrophs and the addition of spent media of some strains, suggesting that not only heterotrophs but also Nitrospira received benefits from their mutual co-existence. Furthermore, the data suggested that some of the growth-promoting heterotrophs provided as-yet-unidentified growth-promoting factors to Nitrospira. Overall, Nitrospira and heterotrophs thus appear to exhibit a mutualistic relationship. Such mutualistic relationships between autotrophs and heterotrophs would contribute to the stability and diversity of microbial ecosystems.

New geochemical tools for investigating resource and energy functions at deep-sea cold seeps using amino acid δ15 N in chemosymbiotic mussels (Bathymodiolus childressi)

In order to reconstruct the ecosystem structure of chemosynthetic environments in the fossil record, geochemical proxies must be developed. Here, we present a suite of novel compound-specific isotope parameters for tracing chemosynthetic production with a focus on understanding nitrogen dynamics in deep-sea cold seep environments. We examined the chemosymbiotic bivalve Bathymodiolus childressi from three geographically distinct seep sites on the NE Atlantic Margin and compared isotope data to non-chemosynthetic littoral mussels to test whether water depth, seep activity, and/or mussel bed size are linked to differences in chemosynthetic production. The bulk isotope analysis of carbon (δ¹³ C) and nitrogen (δ¹⁵ N), and δ¹⁵ N values of individual amino acids (δ¹⁵ N_AA ) in both gill and muscle tissues, as well as δ¹⁵ N_AA- derived parameters including trophic level (TL), baseline δ¹⁵ N value (δ¹⁵ N_Phe ), and a microbial resynthesis index (ΣV), were used to investigate specific geochemical signatures of chemosynthesis. Our results show that δ¹⁵ N_AA values provide a number of new proxies for relative reliance on chemosynthesis, including TL, ∑V, and both δ¹⁵ N values and molar percentages (Gly/Glu mol% index) of specific AA. Together, these parameters suggested that relative chemoautotrophy is linked to both degree of venting from seeps and mussel bed size. Finally, we tested a Bayesian mixing model using diagnostic AA δ¹⁵ N values, showing that percent contribution of chemoautotrophic versus heterotrophic production to seep mussel nutrition can be directly estimated from δ¹⁵ N_AA values. Our results demonstrate that δ¹⁵ N_AA analysis can provide a new set of geochemical tools to better understand mixotrophic ecosystem function and energetics, and suggest extension to the study of ancient chemosynthetic environments in the fossil record.

Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling

BACKGROUND

Coastal aquatic ecosystems include chemically distinct, but highly interconnected environments. Across a freshwater-to-marine transect, aquatic communities are exposed to large variations in salinity and nutrient availability as tidal cycles create periodic fluctuations in local conditions. These factors are predicted to strongly influence the resident microbial community structure and functioning, and alter the structure of aquatic food webs and biogeochemical cycles. Nevertheless, little is known about the spatial distribution of metabolic properties across salinity gradients, and no study has simultaneously surveyed the sediment and water environments. Here, we determined patterns and drivers of benthic and planktonic prokaryotic and microeukaryotic community assembly across a river and tidal lagoon system by collecting sediments and planktonic biomass at nine shallow subtidal sites in the summer. Genomic and transcriptomic analyses, alongside a suite of complementary geochemical data, were used to determine patterns in the distribution of taxa, mechanisms of salt tolerance, and nutrient cycling.

RESULTS

Taxonomic and metabolic profiles related to salt tolerance and nutrient cycling of the aquatic microbiome were found to decrease in similarity with increasing salinity, and distinct trends in diversity were observed between the water column and sediment. Non-saline and saline communities adopted divergent strategies for osmoregulation, with an increase in osmoregulation-related transcript expression as salinity increased in the water column due to lineage-specific adaptations to salt tolerance. Results indicated a transition from phosphate limitation in freshwater habitats to nutrient-rich conditions in the brackish zone, where distinct carbon, nitrogen and sulfur cycling processes dominated. Phosphorus acquisition-related activity was highest in the freshwater zone, along with dissimilatory nitrate reduction to ammonium in freshwater sediment. Activity associated with denitrification, sulfur metabolism and photosynthesis were instead highest in the brackish zone, where photosynthesis was dominated by distinct microeukaryotes in water (Cryptophyta) and sediment (diatoms). Despite microeukaryotes and archaea being rare relative to bacteria, results indicate that they contributed more to photosynthesis and ammonia oxidation, respectively.

CONCLUSIONS

Our study demonstrates clear freshwater-saline and sediment-water ecosystem boundaries in an interconnected coastal aquatic system and provides a framework for understanding the relative importance of salinity, planktonic-versus-benthic habitats and nutrient availability in shaping aquatic microbial metabolic processes, particularly in tidal lagoon systems. Video abstract.

Global co-occurrence of methanogenic archaea and methanotrophic bacteria in Microcystis aggregates

Global warming and eutrophication contribute to the worldwide increase in cyanobacterial blooms, and the level of cyanobacterial biomass is strongly associated with rises in methane emissions from surface lake waters. Hence, methane-metabolizing microorganisms may be important for modulating carbon flow in cyanobacterial blooms. Here, we surveyed methanogenic and methanotrophic communities associated with floating Microcystis aggregates in 10 lakes spanning four continents, through sequencing of 16S rRNA and functional marker genes. Methanogenic archaea (mainly Methanoregula and Methanosaeta) were detectable in 5 of the 10 lakes and constituted the majority (~50%-90%) of the archaeal community in these lakes. Three of the 10 lakes contained relatively more abundant methanotrophs than the other seven lakes, with the methanotrophic genera Methyloparacoccus, Crenothrix, and an uncultured species related to Methylobacter dominating and nearly exclusively found in each of those three lakes. These three are among the five lakes in which methanogens were observed. Operational taxonomic unit (OTU) richness and abundance of methanotrophs were strongly positively correlated with those of methanogens, suggesting that their activities may be coupled. These Microcystis-aggregate-associated methanotrophs may be responsible for a hitherto overlooked sink for methane in surface freshwaters, and their co-occurrence with methanogens sheds light on the methane cycle in cyanobacterial aggregates.

Mimicking biofilm formation and development: Recent progress in in vitro and in vivo biofilm models

Biofilm formation in living organisms is associated to tissue and implant infections, and it has also been linked to the contribution of antibiotic resistance. Thus, understanding biofilm development and being able to mimic such processes is vital for the successful development of antibiofilm treatments and therapies. Several decades of research have contributed to building the foundation for developing in vitro and in vivo biofilm models. However, no such thing as an "all fit" in vitro or in vivo biofilm models is currently available. In this review, in addition to presenting an updated overview of biofilm formation, we critically revise recent approaches for the improvement of in vitro and in vivo biofilm models.

Succession of the Resident Soil Microbial Community in Response to Periodic Inoculations

Introducing beneficial microbes to the plant-soil system is an environmentally friendly approach to improve the crop yield and soil environment. Numerous studies have attempted to reveal the impacts of inoculation on the rhizosphere microbiome.

To maintain the beneficial effects of microbial inoculants on plants and soil, repeated inoculation represents a promising option. Until now, the impacts of one-off inoculation on the native microbiome have been explored, but it remains unclear how long and to what extent the periodic inoculations would affect the succession of the resident microbiome in bulk soil. Here, we examined the dynamic responses of plant growth, soil functions, and the resident bacterial community in the bulk soil to periodic inoculations of phosphate-solubilizing and N₂-fixing bacteria alone or in combination. Compared to single-strain inoculation, coinoculation better stimulated plant growth and soil nutrients. However, the benefits from inoculants did not increase with repeated inoculations and were not maintained after transplantation to a different site. In response to microbial inoculants, three patterns of shifts in the bacterial composition were observed: fold increase, fold decrease, and resilience. The periodic inoculations impacted the succession course of resident bacterial communities in bulk soil, mainly driven by changes in soil pH and nitrate, resulting in the development of three main cluster types throughout the investigation. The single and mixed inoculants transiently modulated the variation in the resident community in association with soil pH and the C/N ratio, but finally, the community established and showed resilience to subsequent inoculations. Consequently, the necessity of repeated inoculations should be reconsidered, and while the different microbial inoculants showed distinct impacts on resident microbiome succession, the communities ultimately exhibited resilience.

IMPORTANCE Introducing beneficial microbes to the plant-soil system is an environmentally friendly approach to improve the crop yield and soil environment. Numerous studies have attempted to reveal the impacts of inoculation on the rhizosphere microbiome. However, little is known about the effectiveness of periodic inoculations on soil functioning. In addition, the long-term impact of repeated inoculations on the native community remains unclear. Here, we track the succession traits of the resident microbiome in the bulk soil across a growing season and identify the taxon clusters that respond differently to periodic inoculation. Crucially, we compare the development of the resident community composition with and without inoculation, thus providing new insight into the interactions between resident microbes and intruders. Finally, we conclude that initial inoculation plays a more important role in influencing the whole system, and the native microbial community exhibits traits of resilience, but no resistance, to the subsequent inoculations.

Geochemical and metagenomics study of a metal-rich, green-turquoise-coloured stream in the southern Swiss Alps

The Swiss Alpine environments are poorly described from a microbiological perspective. Near the Greina plateau in the Camadra valley in Ticino (southern Swiss Alps), a green-turquoise-coloured water spring streams off the mountain cliffs. Geochemical profiling revealed naturally elevated concentrations of heavy metals such as copper, lithium, zinc and cadmium, which are highly unusual for the geomorphology of the region. Of particular interest, was the presence of a thick biofilm, that was revealed by microscopic analysis to be mainly composed of Cyanobacteria. A metagenome was further assembled to detail the genes found in this environment. A multitude of genes for resistance/tolerance to high heavy metal concentrations were indeed found, such as, various transport systems, and genes involved in the synthesis of extracellular polymeric substances (EPS). EPS have been evoked as a central component in photosynthetic environments rich in heavy metals, for their ability to drive the sequestration of toxic, positively-charged metal ions under high regimes of cyanobacteria-driven photosynthesis. The results of this study provide a geochemical and microbiological description of this unusual environment in the southern Swiss Alps, the role of cyanobacterial photosynthesis in metal resistance, and the potential role of such microbial community in bioremediation of metal-contaminated environments.

Graphene-Based Nanomaterials Modulate Internal Biofilm Interactions and Microbial Diversity

Graphene-based nanomaterials (GBMs), such as graphene oxide (GO) and reduced graphene oxide (rGO), possess unique properties triggering high expectations for the development of new technological applications and are forecasted to be produced at industrial-scale. This raises the question of potential adverse outcomes on living organisms and especially toward microorganisms constituting the basis of the trophic chain in ecosystems. However, investigations on GBMs toxicity were performed on various microorganisms using single species that are helpful to determine toxicity mechanisms but fail to predict the consequences of the observed effects at a larger organization scale. Thus, this study focuses on the ecotoxicological assessment of GO and rGO toward a biofilm composed of the diatom Nitzschia palea associated to a bacterial consortium. After 48 and 144 h of exposure to these GBMs at 0, 0.1, 1, and 10 mg.L⁻¹, their effects on the diatom physiology, the structure, and the metabolism of bacterial communities were measured through the use of flow cytometry, 16S amplicon sequencing, and Biolog ecoplates, respectively. The exposure to both of these GBMs stimulated the diatom growth. Besides, GO exerted strong bacterial growth inhibition as from 1 mg.L⁻¹, influenced the taxonomic composition of diatom-associated bacterial consortium, and increased transiently the bacterial activity related to carbon cycling, with weak toxicity toward the diatom. On the contrary, rGO was shown to exert a weaker toxicity toward the bacterial consortium, whereas it influenced more strongly the diatom physiology. When compared to the results from the literature using single species tests, our study suggests that diatoms benefited from diatom-bacteria interactions and that the biofilm was able to maintain or recover its carbon-related metabolic activities when exposed to GBMs.

Bioturbation by the marine polychaete Capitella teleta alters the sediment microbial community by ingestion and defecation of sediment particles

Deposit-feeding benthic invertebrates are known to modify sediment structure and impact microbial processes associated with biogeochemical cycles in marine sedimentary environments. Despite this, however, there is limited information on how sediment ingestion and defecation by marine benthos alters microbial community structure and function in sediments. In the current study, we used high-throughput sequencing data of 16S rRNA genes obtained from a previous microcosm study to examine how sediment processing by the marine polychaete Capitella teleta specifically affects sediment microbiota. Here we show that both sediment ingestion and defecation by C. teleta significantly alters overall microbial community structure and function. Sediment processing by C. teleta resulted in significant enrichment of sediment microbial communities involved in sulfur and carbon cycling in worm fecal pellets. Moreover, C. teleta's microbiota was predominantly comprised of bacterial functional groups involved in fermentation, relative to microbiota found outside of the host. Collectively, results of this study indicate that C. teleta has the ability to alter microbial biogeochemical cycles in the benthic sedimentary environment by altering microbial assemblages in the worm gut, and in the sediment ingested and defecated by worms as they feed on sediment particles. In this sense, C. teleta plays an important role as an ecosystem engineer and in shaping nutrient cycling in the benthic environment.

Study on the isoprene-producing co-culture system of Synechococcus elongates-Escherichia coli through omics analysis

BACKGROUND

The majority of microbial fermentations are currently performed in the batch or fed-batch manner with the high process complexity and huge water consumption. The continuous microbial production can contribute to the green sustainable development of the fermentation industry. The co-culture systems of photo-autotrophic and heterotrophic species can play important roles in establishing the continuous fermentation mode for the bio-based chemicals production.

RESULTS

In the present paper, the co-culture system of Synechococcus elongates-Escherichia coli was established and put into operation stably for isoprene production. Compared with the axenic culture, the fermentation period of time was extended from 100 to 400 h in the co-culture and the isoprene production was increased to eightfold. For in depth understanding this novel system, the differential omics profiles were analyzed. The responses of BL21(DE3) to S. elongatus PCC 7942 were triggered by the oxidative pressure through the Fenton reaction and all these changes were linked with one another at different spatial and temporal scales. The oxidative stress mitigation pathways might contribute to the long-lasting fermentation process. The performance of this co-culture system can be further improved according to the fundamental rules discovered by the omics analysis.

CONCLUSIONS

The isoprene-producing co-culture system of S. elongates-E. coli was established and then analyzed by the omics methods. This study on the co-culture system of the model S. elongates-E. coli is of significance to reveal the common interactions between photo-autotrophic and heterotrophic species without natural symbiotic relation, which could provide the scientific basis for rational design of microbial community.

Iron Flocs and the Three Domains: Microbial Interactions in Freshwater Iron Mats

Freshwater iron mats are dynamic geochemical environments with broad ecological diversity, primarily formed by the iron-oxidizing bacteria. The community features functional groups involved in biogeochemical cycles for iron, sulfur, carbon, and nitrogen. Despite this complexity, iron mat communities provide an excellent model system for exploring microbial ecological interactions and ecological theories in situ Syntrophies and competition between the functional groups in iron mats, how they connect cycles, and the maintenance of these communities by taxons outside bacteria (the eukaryota, archaea, and viruses) have been largely unstudied. Here, we review what is currently known about freshwater iron mat communities, the taxa that reside there, and the interactions between these organisms, and we propose ways in which future studies may uncover exciting new discoveries. For example, the archaea in these mats may play a greater role than previously thought as they are diverse and widespread in iron mats based on 16S rRNA genes and include methanogenic taxa. Studies with a holistic view of the iron mat community members focusing on their diverse interactions will expand our understanding of community functions, such as those involved in pollution removal. To begin addressing questions regarding the fundamental interactions and to identify the conditions in which they occur, more laboratory culturing techniques and coculture studies, more network and keystone species analyses, and the expansion of studies to more freshwater iron mat systems are necessary. Increasingly accessible bioinformatic, geochemical, and culturing tools now open avenues to address the questions that we pose herein.

The microalga Haematococcus lacustris (Chlorophyceae) forms natural biofilms in supralittoral White Sea coastal rock ponds

Haematococcus lacustris inhabits supralittoral rock ponds and forms, under natural conditions, biofilms including layered cyanobacterial and fermentative microbial mats. Dry mats, formed under extremely stressful conditions, contained only haematocysts. Under favorable growth conditions, modeled for dry biofilms in vitro, microalgal free-living stages were detected. Haematococcus lacustris is the microalga known for its high potential to survive under a wide range of unfavorable conditions, particularly in the supralittoral temporal rock ponds of the White Sea. Previously, we described microbial communities containing H. lacustris in this region. In many cases, they were organized into systems exhibiting complex three-dimensional structure similar to that of natural biofilms. In this study, for the first time, we clarify structural description and provide microscopic evidence that these communities of H. lacustris and bacteria are assembled into the true biofilms. There are (1) simple single layer biofilms on the surface of rocks and macrophytic algae, (2) floccules (or flocs) not attached to a surface, (3) as well as stratified (layered) biofilms, wet, and dehydrated in nature. Being involved into primary organic production, H. lacustris and cyanobacteria are located exclusively in the upper layers of stratified biofilms, where they are capable to absorb sufficient for photosynthesis amount of light. The presence of acidic polysaccharides in the extracellular matrix revealed by specific staining with ruthenium red in the H. lacustris-containing microbial communities is a biochemical evidence of biofilm formation. Meanwhile, the presence of bacterial L-form is an ultrastructural confirmation of that fact. Under favorable conditions, modeled in vitro, H. lacustris from the dry microbial mats moves to the free-living states represented by vegetative palmelloid cells and motile zoospores. Owing to the fact that inside biofilms cells of microorganisms exist under stable conditions, we consider the biofilm formation as an additional mechanism that contributes to the survival of H. lacustris in the supralittoral zone of the White Sea.

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

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

Trichoderma virens Gl006 and Bacillus velezensis Bs006: a compatible interaction controlling Fusarium wilt of cape gooseberry

The combination of Trichoderma virens Gl006 and B. velezensis Bs006 as a consortium has high potential to control Fusarium wilt (FW) of cape gooseberry (Physalis peruviana) caused by Fusarium oxysporum f. sp. physali (Foph). However, the interactions between these two microorganisms that influence the biocontrol activity as a consortium have not been studied. Here, we studied the interactions between Gl006 and Bs006 that keep their compatibility under in vitro and greenhouse conditions. Antagonism tests between Gl006 and Bs006 inoculated both individually and in consortium against Foph strain Map5 was carried out on several solid media. The effect of supernatant of each selected microorganism on growth, conidia germination, biofilm formation and antagonistic activity on its partner was also studied. Biocontrol activity by different combinations of cells and supernatants from both microorganisms against Fusarium wilt was evaluated under greenhouse conditions. In vitro antagonism of the consortium against Foph showed a differential response among culture media and showed compatibility among BCA under nutritional conditions close to those of the rhizosphere. The supernatant of Bs006 did not affect the antagonistic activity of Gl006 and vice versa. However, the supernatant of Bs006 promoted the biocontrol activity of Gl006 in a synergistic way under greenhouse, reducing the disease severity by 71%. These results prove the compatibility between T. virens Gl006 and B. velezensis Bs006 as a potential tool to control Fusarium wilt of cape gooseberry.

Fitness and Productivity Increase with Ecotypic Diversity among Escherichia coli Strains That Coevolved in a Simple, Constant Environment

The productivity of a biological community often correlates with its diversity. In the microbial world this phenomenon can sometimes be explained by positive, density-dependent interactions such as cross-feeding and syntrophy. These metabolic interactions help account for the astonishing variety of microbial life and drive many of the biogeochemical cycles without which life as we know it could not exist. While it is difficult to recapitulate experimentally how these interactions evolved among multiple taxa, we can explore in the laboratory how they arise within one. These experiments provide insight into how different bacterial ecotypes evolve and from these, possibly new "species." We have previously shown that in a simple, constant environment a single clone of Escherichia coli can give rise to a consortium of genetically and phenotypically differentiated strains, in effect, a set of ecotypes, that coexist by cross-feeding. We marked these different ecotypes and their shared ancestor by integrating fluorescent protein into their genomes and then used flow cytometry to show that each evolved strain is more fit than the shared ancestor, that pairs of evolved strains are fitter still, and that the entire consortium is the fittest of all. We further demonstrate that the rank order of fitness values agrees with estimates of yield, indicating that an experimentally evolved consortium more efficiently converts primary and secondary resources to offspring than its ancestor or any member acting in isolation.IMPORTANCE Polymicrobial consortia occur in both environmental and clinical settings. In many cases, diversity and productivity correlate in these consortia, especially when sustained by positive, density-dependent interactions. However, the evolutionary history of such entities is typically obscure, making it difficult to establish the relative fitness of consortium partners and to use those data to illuminate the diversity-productivity relationship. Here, we dissect an Escherichia coli consortium that evolved under continuous glucose limitation in the laboratory from a single common ancestor. We show that a partnership consisting of cross-feeding ecotypes is better able to secure primary and secondary resources and to convert those resources to offspring than the ancestral clone. Such interactions may be a prelude to a special form of syntrophy and are likely determinants of microbial community structure in nature, including those having clinical significance such as chronic infections.

Mixed-habitat assimilation of organic waste in coastal environments - It's all about synergy!

Fish farms are increasingly situated in strong current sites above or near to mixed-bottom habitats that include organisms not normally considered in the context of organic enrichment. This study takes a holistic view of the benthic enrichment process by combining different survey techniques on complimentary spatial scales: conventional macrofaunal cores, larger-scale visual quantification of epibiota and environmental-DNA metabarcoding of microbial communities. A large tube forming polychaete (Arenicola marina), normally found intertidally and living too deep for conventional sampling, was observed occupying an opportunistic niche in areas of high deposition and in very close association with Capitellid worm complexes. The surface-dwelling brittlestar, Ophiocomina nigra, was abundant at distances of 250-1000 m from Farm-B, suggesting a positive response to enrichment, but was displaced where sedimentation exceed 5 g m² d^-1. A corresponding gradient was evident within the sediment microbial communities, supporting established theories about ecosystem engineering and multi-species synergies for organic waste assimilation. Many of the bacteria present in the near-farm sediments were linked to the farmed fish and fish health issues suggesting one or two-way inoculation pressures. These functionally different benthic organisms are intrinsically linked and the resulting synergy has the potential to assimilate significant quantities of anthropogenically produced organic waste contributing to environmental sustainability.

Species Interaction and Selective Carbon Addition During Antibiotic Exposure Enhances Bacterial Survival

Biofilms are multifaceted and robust microbiological systems that enable microorganisms to withstand a multitude of environmental stresses and expand their habitat range. We have shown previously that nutritional status alters antibiotic susceptibility in a mixed-species biofilm. To further elucidate the effects of nutrient addition on inter-species dynamics and whole-biofilm susceptibility to high-dose streptomycin exposures, a CO₂ Evolution Measurement System was used to monitor the metabolic activity of early steady state pure-culture and mixed-species biofilms containing Pseudomonas aeruginosa and Stenotrophomonas maltophilia, with and without added carbon. Carbon supplementation was needed for biofilm recovery from high-dose streptomycin exposures when P. aeruginosa was either the dominant community member in a mixed-species biofilm (containing predominantly P. aeruginosa and S. maltophilia) or as a pure culture. By contrast, S. maltophilia biofilms could recover from high-dose streptomycin exposures without the need for carbon addition during antibiotic exposure. Metagenomic analysis revealed that even when inocula were dominated by Pseudomonas, the relative abundance of Stenotrophomonas increased upon biofilm development to ultimately become the dominant species post-streptomycin exposure. The combined metabolic and metagenomic results demonstrated the relevance of inter-species influence on survival and that nutritional status has a strong influence on the survival of P. aeruginosa dominated biofilms.

Community-level respiration of prokaryotic microbes may rise with global warming

Understanding how the metabolic rates of prokaryotes respond to temperature is fundamental to our understanding of how ecosystem functioning will be altered by climate change, as these micro-organisms are major contributors to global carbon efflux. Ecological metabolic theory suggests that species living at higher temperatures evolve higher growth rates than those in cooler niches due to thermodynamic constraints. Here, using a global prokaryotic dataset, we find that maximal growth rate at thermal optimum increases with temperature for mesophiles (temperature optima [Formula: see text]C), but not thermophiles ([Formula: see text]C). Furthermore, short-term (within-day) thermal responses of prokaryotic metabolic rates are typically more sensitive to warming than those of eukaryotes. Because climatic warming will mostly impact ecosystems in the mesophilic temperature range, we conclude that as microbial communities adapt to higher temperatures, their metabolic rates and therefore, biomass-specific CO[Formula: see text] production, will inevitably rise. Using a mathematical model, we illustrate the potential global impacts of these findings.

Putative Mixotrophic Nitrifying-Denitrifying Gammaproteobacteria Implicated in Nitrogen Cycling Within the Ammonia/Oxygen Transition Zone of an Oil Sands Pit Lake

Anthropogenically-impacted environments offer the opportunity to discover novel microbial species and metabolisms, which may be undetectable in natural systems. Here, a combined metagenomic and geochemical study in Base Mine Lake, Alberta, Canada, which is the only oil sands end pit lake to date, revealed that nitrification was performed by members from Nitrosomonadaceae, Chloroflexi and unclassified Gammaproteobacteria “MBAE14.” While Nitrosomonadaceae and Chloroflexi groups were relatively abundant in the upper oxygenated zones, MBAE14 dominated the hypoxic hypolimnetic zones (approximately 30% of total microbial communities); MBAE14 was not detected in the underlying anoxic tailings. Replication rate analyses indicate that MBAE14 grew in metalimnetic and hypolimnetic water cap regions, most actively at the metalimnetic, ammonia/oxygen transition zone consistent with it putatively conducting nitrification. Detailed genomic analyses of MBAE14 evidenced both ammonia oxidation and denitrification into dinitrogen capabilities. However, the absence of known CO₂-fixation genes suggests a heterotrophic denitrifying metabolism. Functional marker genes of ammonia oxidation (amo and hao) in the MBAE14 genome are homologous with those conserved in autotrophic nitrifiers, but not with those of known heterotrophic nitrifiers. We propose that this novel MBAE14 inhabits the specific ammonia-rich, oxygen and labile organic matter-limited conditions occurring in Base Mine Lake which selectively favors mixotrophic coupled nitrifier denitrification metabolism. Our results highlight the opportunities to better constrain biogeochemical cycles from the application of metagenomics to engineered systems associated with extractive resource sectors.

Distinct nitrogen cycling and steep chemical gradients in Trichodesmium colonies

Trichodesmium is an important dinitrogen (N₂)-fixing cyanobacterium in marine ecosystems. Recent nucleic acid analyses indicate that Trichodesmium colonies with their diverse epibionts support various nitrogen (N) transformations beyond N₂ fixation. However, rates of these transformations and concentration gradients of N compounds in Trichodesmium colonies remain largely unresolved. We combined isotope-tracer incubations, micro-profiling and numeric modelling to explore carbon fixation, N cycling processes as well as oxygen, ammonium and nitrate concentration gradients in individual field-sampled Trichodesmium colonies. Colonies were net-autotrophic, with carbon and N₂ fixation occurring mostly during the day. Ten percent of the fixed N was released as ammonium after 12-h incubations. Nitrification was not detectable but nitrate consumption was high when nitrate was added. The consumed nitrate was partly reduced to ammonium, while denitrification was insignificant. Thus, the potential N transformation network was characterised by fixed N gain and recycling processes rather than denitrification. Oxygen concentrations within colonies were ~60-200% air-saturation. Moreover, our modelling predicted steep concentration gradients, with up to 6-fold higher ammonium concentrations, and nitrate depletion in the colony centre compared to the ambient seawater. These gradients created a chemically heterogeneous microenvironment, presumably facilitating diverse microbial metabolisms in millimetre-sized Trichodesmium colonies.

The Vulnerability of Microbial Ecosystems in A Changing Climate: Potential Impact in Shark Bay

The potential impact of climate change on eukaryotes, including humans, has been relatively well described. In contrast, the contribution and susceptibility of microorganisms to a changing climate have, until recently, received relatively less attention. In this review, the importance of microorganisms in the climate change discourse is highlighted. Microorganisms are responsible for approximately half of all primary production on earth, support all forms of macroscopic life whether directly or indirectly, and often persist in “extreme” environments where most other life are excluded. In short, microorganisms are the life support system of the biosphere and therefore must be included in decision making regarding climate change. Any effects climate change will have on microorganisms will inevitably impact higher eukaryotes and the activity of microbial communities in turn can contribute to or alleviate the severity of the changing climate. It is of vital importance that unique, fragile, microbial ecosystems are a focus of research efforts so that their resilience to extreme weather events and climate change are thoroughly understood and that conservation efforts can be implemented as a response. One such ecosystem under threat are the evolutionarily significant microbial mats and stromatolites, such as those present in Shark Bay, Western Australia. Climate change models have suggested the duration and severity of extreme weather events in this region will increase, along with rising temperatures, sea levels, and ocean acidification. These changes could upset the delicate balance that fosters the development of microbial mats and stromatolites in Shark Bay. Thus, the challenges facing Shark Bay microbial communities will be presented here as a specific case study.

Integrated Effects of Co-Inoculation with Phosphate-Solubilizing Bacteria and N2-Fixing Bacteria on Microbial Population and Soil Amendment Under C Deficiency

The inoculation of beneficial microorganisms to improve plant growth and soil properties is a promising strategy in the soil amendment. However, the effects of co-inoculation with phosphate-solubilizing bacteria (PSB) and N₂-fixing bacteria (NFB) on the soil properties of typical C-deficient soil remain unclear. Based on a controlled experiment and a pot experiment, we examined the effects of PSB (M: Bacillus megaterium and F: Pseudomonas fluorescens), NFB (C: Azotobacter chroococcum and B: Azospirillum brasilence), and combined PSB and NFB treatments on C, N, P availability, and enzyme activities in sterilized soil, as well as the growth of Cyclocarya Paliurus seedlings grow in unsterilized soil. During a 60-day culture, prominent increases in soil inorganic N and available P contents were detected after bacteria additions. Three patterns were observed for different additions according to the dynamic bacterial growth. Synergistic effects between NFB and PSB were obvious, co-inoculations with NFB enhanced the accumulation of available P. However, decreases in soil available P and N were observed on the 60th day, which was induced by the decreases in bacterial quantities under C deficiency. Besides, co-inoculations with PSB and NFB resulted in greater performance in plant growth promotion. Aimed at amending soil with a C supply shortage, combined PSB and NFB treatments are more appropriate for practical fertilization at intervals of 30–45 days. The results demonstrate that co-inoculations could have synergistic interactions during culture and application, which may help with understanding the possible mechanism of soil amendment driven by microorganisms under C deficiency, thereby providing an alternative option for amending such soil.

Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales

Soils contain a tangle of minerals, water, nutrients, gases, plant roots, decaying organic matter, and microorganisms which work together to cycle nutrients and support terrestrial plant growth. Most soil microorganisms live in periodically interconnected communities closely associated with soil aggregates, i.e., small (<2 mm), strongly bound clusters of minerals and organic carbon that persist through mechanical disruptions and wetting events. Their spatial structure is important for biogeochemical cycling, and we cannot reliably predict soil biological activities and variability by studying bulk soils alone. To fully understand the biogeochemical processes at work in soils, it is necessary to understand the micrometer-scale interactions that occur between soil particles and their microbial inhabitants. Here, we review the current state of knowledge regarding soil aggregate microbial communities and identify areas of opportunity to study soil ecosystems at a scale relevant to individual cells. We present a framework for understanding aggregate communities as "microbial villages" that are periodically connected through wetting events, allowing for the transfer of genetic material, metabolites, and viruses. We describe both top-down (whole community) and bottom-up (reductionist) strategies for studying these communities. Understanding this requires combining "model system" approaches (e.g., developing mock community artificial aggregates), field observations of natural communities, and broader study of community interactions to include understudied community members, like viruses. Initial studies suggest that aggregate-based approaches are a critical next step for developing a predictive understanding of how geochemical and community interactions govern microbial community structure and nutrient cycling in soil.

In Silico Metabolic Design of Two-Strain Biofilm Systems Predicts Enhanced Biomass Production and Biochemical Synthesis

Engineered biofilm consortia have the potential to solve important biotechnological problems that have proved difficult for monoculture biofilms and planktonic consortia, such as conversion of lignocellulosic material to useful biochemicals. While considerable experimental progress has been reported for engineering and characterizing biofilm consortia, the field still lacks in silico tools for simulation, design, and optimization of stable, robust, and productive designed consortia. We developed biofilm consortia metabolic models for two coculture systems centered around the ecological design motif of a primary cell type that utilizes a supplied electron donor and secretes acetate as a byproduct and a secondary cell type that consumes the acetate, relieving byproduct inhibition on the primary cell type and enhancing overall system biomass. The models presented in this paper predict that distinct metabolic niches for the two cell types could be established by supplying electron donors and acceptors at opposite ends of the biofilm and that acetate consumption by the secondary cell type could increase total biomass accumulation and the synthesis of valuable biochemicals, such as isobutanol, by the primary cell type. System tunability is enhanced when each cell type is supplied with a unique terminal electron acceptor at opposite ends of the biofilm rather than competing for a common electron acceptor. Our model provides good qualitative agreement with data for a synthetic Escherichia coli coculture system, suggesting that the proposed design rules may have wide applicability to engineered biofilm consortia.

Identification of ability to form biofilm in Candida parapsilosis and Staphylococcus epidermidis by Raman spectroscopy

Aim: Finding rapid, reliable diagnostic methods is a big challenge in clinical microbiology. Raman spectroscopy is an optical method used for multiple applications in scientific fields including microbiology. This work reports its potential in identifying biofilm positive strains of Candida parapsilosis and Staphylococcus epidermidis. Materials & methods: We tested 54 S. epidermidis strains (23 biofilm positive, 31 negative) and 51 C. parapsilosis strains (27 biofilm positive, 24 negative) from colonies on Mueller-Hinton agar plates, using Raman spectroscopy. Results: The accuracy was 98.9% for C. parapsilosis and 96.1% for S. epidermidis. Conclusion: The method showed great potential for identifying biofilm positive bacterial and yeast strains. We suggest that Raman spectroscopy might become a useful aid in clinical diagnostics.

Microbial community composition and dolomite formation in the hypersaline microbial mats of the Khor Al-Adaid sabkhas, Qatar

The Khor Al-Adaid sabkha in Qatar is among the rare extreme environments on Earth where it is possible to study the formation of dolomite-a carbonate mineral whose origin remains unclear and has been hypothetically linked to microbial activity. By combining geochemical measurements with microbiological analysis, we have investigated the microbial mats colonizing the intertidal areas of sabhka. The main aim of this study was to identify communities and conditions that are favorable for dolomite formation. We inspected and sampled two locations. The first site was colonized by microbial mats that graded vertically from photo-oxic to anoxic conditions and were dominated by cyanobacteria. The second site, with higher salinity, had mats with an uppermost photo-oxic layer dominated by filamentous anoxygenic photosynthetic bacteria (FAPB), which potentially act as a protective layer against salinity for cyanobacterial species within the deeper layers. Porewater in the uppermost layers of the both investigated microbial mats was supersaturated with respect to dolomite. Corresponding to the variation of the microbial community's vertical structure, a difference in crystallinity and morphology of dolomitic phases was observed: dumbbell-shaped proto-dolomite in the mats dominated by cyanobacteria and rhombohedral ordered-dolomite in the mat dominated by FAPB.

Implications of denitrification in the ecological status of an urban river using enzymatic activities in sediments as an indicator

A better understanding of the effects of a number of environmental factors on denitrification is vital for analyzing its role as nitrogen sink and providing deeper knowledge about the ecological status of a nitrate-rich ecosystem. Since few studies have addressed the occurrence and implications of denitrification in river sediments, and complexity of interactions among all these environmental factors makes comprehension of the process difficult, the potential of sediments from the Deba River to attenuate nitrate excess through denitrification was investigated. For this purpose, we adapted an in vitro method to measure activities of two enzymes contributing to the entire multiple-step nitrate reduction: Nitrate Reductase and Nitrite Reductase. The environmental features that influence both or single enzymatic activities were identified as oxygen availability, regulated directly by the moisture content or indirectly through the aerobic respiration, organic matter and nitrate content of sediments, and electrical conductivity and exchangeable sodium percentage of water. Additionally, our results showed that Nitrate Reductase catalyzes the principal limiting step of denitrification in sediments. Therefore, taking this enzymatic activity as an indicator, the southern part of the Deba River catchment presented low potential to denitrify but nitrate-limited sediments, whereas the middle and northern parts were characterized by high denitrification potential but nitrate-rich sediments. In general, this study on denitrifying enzymatic activities in sediments evaluates the suitability of the management of the effluents from wastewater treatment plants and municipal sewages to ensure a good ecological status of the Deba River.

Single-cell imaging of phosphorus uptake shows that key harmful algae rely on different phosphorus sources for growth

Single-cell measurements of biochemical processes have advanced our understanding of cellular physiology in individual microbes and microbial populations. Due to methodological limitations, little is known about single-cell phosphorus (P) uptake and its importance for microbial growth within mixed field populations. Here, we developed a nanometer-scale secondary ion mass spectrometry (nanoSIMS)-based approach to quantify single-cell P uptake in combination with cellular CO₂ and N₂ fixation. Applying this approach during a harmful algal bloom (HAB), we found that the toxin-producer Nodularia almost exclusively used phosphate for growth at very low phosphate concentrations in the Baltic Sea. In contrast, the non-toxic Aphanizomenon acquired only 15% of its cellular P-demand from phosphate and ~85% from organic P. When phosphate concentrations were raised, Nodularia thrived indicating that this toxin-producer directly benefits from phosphate inputs. The phosphate availability in the Baltic Sea is projected to rise and therefore might foster more frequent and intense Nodularia blooms with a concomitant rise in the overall toxicity of HABs in the Baltic Sea. With a projected increase in HABs worldwide, the capability to use organic P may be a critical factor that not only determines the microbial community structure, but the overall harmfulness and associated costs of algal blooms.