Temporal and Spatial Distribution of the Microbial Community of Winogradsky Columns

Energy-ordered resource stratification as an agnostic signature of life

The search for extraterrestrial life hinges on identifying biosignatures, often focusing on gaseous metabolic byproducts as indicators. However, most such biosignatures require assuming specific metabolic processes. It is widely recognized that life on other planets may not resemble that of Earth, but identifying biosignatures "agnostic" to such assumptions has remained a challenge. Here, we propose a novel approach by considering the generic outcome of life: the formation of competing ecosystems. We use a minimal model to argue that the presence of ecosystem-level dynamics, characterized by ecological interactions and resource competition, may yield biosignatures independent of specific metabolic activities. Specifically, we propose the emergent stratification of chemical resources in order of decreasing energy content as a candidate new biosignature. While likely inaccessible to remote sensing, this signature could be relevant for sample return missions, or for detection of ancient signatures of life on Earth itself.

Colon or semicolon: gut sampling microdevices for omics insights

Ingestible microdevices represent a breakthrough in non-invasive sampling of the human gastrointestinal (GI) tract. By capturing the native spatiotemporal microbiome and intricate biochemical gradients, these devices allow a non-invasive multi-omic access to the unperturbed host-microbiota crosstalk, immune/nutritional landscapes and gut-organ connections. We present the current progress of GI sampling microdevices towards personalized metabolism and fostering collaboration among clinicians, engineers, and data scientists.

Bacterial phenotypic heterogeneity through the lens of single-cell RNA sequencing

Bacterial transcription is not monolithic. Microbes exist in a wide variety of cell states that help them adapt to their environment, acquire and produce essential nutrients, and engage in both competition and cooperation with their neighbors. While we typically think of bacterial adaptation as a group behavior, where all cells respond in unison, there is often a mixture of phenotypic responses within a bacterial population, where distinct cell types arise. A primary phenomenon driving these distinct cell states is transcriptional heterogeneity. Given that bacterial mRNA transcripts are extremely short-lived compared to eukaryotes, their transcriptional state is closely associated with their physiology, and thus the transcriptome of a bacterial cell acts as a snapshot of the behavior of that bacterium. Therefore, the application of single-cell transcriptomics to microbial populations will provide novel insight into cellular differentiation and bacterial ecology. In this review, we provide an overview of transcriptional heterogeneity in microbial systems, discuss the findings already provided by single-cell approaches, and plot new avenues of inquiry in transcriptional regulation, cellular biology, and mechanisms of heterogeneity that are made possible when microbial communities are analyzed at single-cell resolution.

Energy harvesting from plants using hybrid microbial fuel cells; potential applications and future exploitation

Microbial Fuel Cells (MFC) can be fuelled using biomass derived from dead plant material and can operate on plant produced chemicals such as sugars, carbohydrates, polysaccharides and cellulose, as well as being "fed" on a regular diet of primary biomass from plants or algae. An even closer relationship can exist if algae (e.g., prokaryotic microalgae or eukaryotic and unicellular algae) can colonise the open to air cathode chambers of MFCs driving photosynthesis, producing a high redox gradient due to the oxygenic phase of collective algal cells. The hybrid system is symbiotic; the conditions within the cathodic chamber favour the growth of microalgae whilst the increased redox and production of oxygen by the algae, favour a more powerful cathode giving a higher maximum voltage and power to the photo-microbial fuel cell, which can ultimately be harvested for a range of end-user applications. MFCs can utilise a wide range of plant derived materials including detritus, plant composts, rhizodeposits, root exudates, dead or dying macro- or microalgae, via Soil-based Microbial Fuel Cells, Sediment Microbial Fuel Cells, Plant-based microbial fuel cells, floating artificial islands and constructed artificial wetlands. This review provides a perspective on this aspect of the technology as yet another attribute of the benevolent Bioelectrochemical Systems.

Iron plaque formation and its influences on the properties of polyethylene plastic surfaces in coastal wetlands: Abiotic factors and bacterial community

Iron (Fe) plaques in coastal wetlands are widely recognized because of their strong adsorption affinity for natural particles, but their interaction behaviors and mechanisms with plastics remain unknown. Through laboratory incubation experiments, paired with multiple characterization methods and microbial analysis, this work focused on the characteristics of Fe plaques on low-density polyethylene plastic surfaces and their relationship with environmental factors in coastal wetlands (Mangrove and Spartina alterniflora soil). The results showed that iron plaques increased the adhesive force of the plastic surface from 65.25 to 300 nN and promoted the oxidation of the plastic surface. Fe plaque formation was stimulated by salinity, anaerobic conditions, natural organic matter, and a weak alkaline scenario (pH 8.0-8.3). The Fe content showed a stable positive correlation with heavy metals loading (i.e., As, Mn, Co, Cr, Pb, and Zn). Furthermore, we revealed that Fe plaque was positively regulated by Nitrospirae through 16S rRNA high-throughput sequencing analysis. Meanwhile, Verrucomicrobia and Kiritimatiellaeota. may act as depressants by consuming salt. This work illustrated that iron plaques could enhance the role of plastics in contaminant migration by altering their adsorption performance, providing new insights into plastic interface behavior and potential ecological effects in coastal wetlands.

Closed ecosystems extract energy through self-organized nutrient cycles

Our planet is a self-sustaining ecosystem powered by light energy from the sun, but roughly closed to matter. Many ecosystems on Earth are also approximately closed to matter and recycle nutrients by self-organizing stable nutrient cycles, e.g., microbial mats, lakes, open ocean gyres. However, existing ecological models do not exhibit the self-organization and dynamical stability widely observed in such planetary-scale ecosystems. Here, we advance a conceptual model that explains the self-organization, stability, and emergent features of closed microbial ecosystems. Our model incorporates the bioenergetics of metabolism into an ecological framework. By studying this model, we uncover a crucial thermodynamic feedback loop that enables metabolically diverse communities to almost always stabilize nutrient cycles. Surprisingly, highly diverse communities self-organize to extract [Formula: see text]10[Formula: see text] of the maximum extractable energy, or [Formula: see text]100 fold more than randomized communities. Further, with increasing diversity, distinct ecosystems show strongly correlated fluxes through nutrient cycles. However, as the driving force from light increases, the fluxes of nutrient cycles become more variable and species-dependent. Our results highlight that self-organization promotes the efficiency and stability of complex ecosystems at extracting energy from the environment, even in the absence of any centralized coordination.

Ecology theory disentangles microbial dichotomies

Microbes are often discussed in terms of dichotomies such as copiotrophic/oligotrophic and fast/slow-growing microbes, defined using the characterisation of microbial growth in isolated cultures. The dichotomies are usually qualitative and/or study-specific, sometimes precluding clear-cut results interpretation. We can unravel microbial dichotomies as life history strategies by combining ecology theory with Monod curves, a laboratory mathematical tool of bacterial physiology that relates the specific growth rate of a microbe with the concentration of a limiting nutrient. Fitting of Monod curves provides quantities that directly correspond to key parameters in ecological theories addressing species coexistence and diversity, such as r/K selection theory, resource competition and community structure theory and the CSR triangle of life strategies. The resulting model allows us to reconcile the copiotrophic/oligotrophic and fast/slow-growing dichotomies as different subsamples of a life history strategy triangle that also includes r/K strategists. We also used the number of known carbon sources together with community structure theory to partially explain the diversity of heterotrophic microbes observed in metagenomics experiments. In sum, we propose a theoretical framework for the study of natural microbial communities that unifies several existing proposals. Its application would require the integration of metagenomics, metametabolomics, Monod curves and carbon source data.

Statistically learning the functional landscape of microbial communities

Microbial consortia exhibit complex functional properties in contexts ranging from soils to bioreactors to human hosts. Understanding how community composition determines function is a major goal of microbial ecology. Here we address this challenge using the concept of community-function landscapes-analogues to fitness landscapes-that capture how changes in community composition alter collective function. Using datasets that represent a broad set of community functions, from production/degradation of specific compounds to biomass generation, we show that statistically inferred landscapes quantitatively predict community functions from knowledge of species presence or absence. Crucially, community-function landscapes allow prediction without explicit knowledge of abundance dynamics or interactions between species and can be accurately trained using measurements from a small subset of all possible community compositions. The success of our approach arises from the fact that empirical community-function landscapes appear to be not rugged, meaning that they largely lack high-order epistatic contributions that would be difficult to fit with limited data. Finally, we show that this observation holds across a wide class of ecological models, suggesting community-function landscapes can be efficiently inferred across a broad range of ecological regimes. Our results open the door to the rational design of consortia without detailed knowledge of abundance dynamics or interactions.

Carbonate precipitation and nitrogen fixation in AMG (Artificial Martian Ground) by cyanobacteria

This article describes experiments performed to study the survival, growth, specific adaptations and bioremediation potential of certain extreme cyanobacteria strains within a simulation of the atmospheric composition, temperature and pressure expected in a future Martian greenhouse. Initial species have been obtained from Mars-analogue sites in Georgia. The results clearly demonstrate that specific biochemical adaptations allow these autotrophs to metabolize within AMG (Artificial Martian Ground) and accumulate biogenic carbon and nitrogen. These findings may thus contribute to the development of future Martian agriculture, as well as other aspects of the life-support systems at habitable Mars stations. The study shows that carbonate precipitation and nitrogen fixation, performed by cyanobacterial communities thriving within the simulated Martian greenhouse conditions, are cross-linked biological processes. At the same time, the presence of the perchlorates (at low concentrations) in the Martian ground may serve as the initial source of oxygen and, indirectly, hydrogen via photo-Fenton reactions. Various carbonates, ammonium and nitrate salts were obtained as the result of these experiments. These affect the pH, salinity and solubility of the AMG and its components, and so the AMG's scanty biogenic properties improved, which is essential for the sustainable growth of the agricultural crops. Therefore, the use of microorganisms for the biological remediation and continuous in situ fertilization of Artificial Martian Ground is possible.

Sustainable removal of soil arsenic by naturally-formed iron oxides on plastic tubes

Arsenic (As) pollution in paddy fields is a major threat to rice safety. Existing As remediation techniques are costly, require external chemical addition and degrade soil properties. Here, we report the use of plastic tubes as a recyclable tool to precisely extract As from contaminated soils. Following insertion into flooded paddy soils, polyethylene tube walls were covered by thin but massive Fe coatings of 76.9-367 mg Fe m^-2 in 2 weeks, which adsorbed significant amounts of As. The formation of tube-wall Fe oxides was driven by local Fe-oxidizing bacteria with oxygen produced by oxygenic phototrophs (e.g., Cyanobacteria) or diffused from air through the tube wall. The tubes with As-bound Fe oxides can be easily separated from soil and then washed and reused. We tested the As removal efficiency in a pot experiment to remove As from ~ 20 cm depth/40 kg soils in a 2-year experiment and achieved an overall removal efficiency of 152 mg As m^-2 soil year^-1, comparable to phytoremediation with the As hyperaccumulator Pteris vittata. The cost of Fe hooks was estimated at 8325 RMB ha^-1 year^-1, and the profit of growing rice (around 16080 RMB ha^-1 year^-1 can be still maintained. The As accumulated in rice tissues was markedly decreased in the treatment (>11.1 %). This work provides a low-cost and sustainable soil remediation method for the targeted removal of As from soils and a useful tool for the study and management of the biogeochemical Fe cycle in paddy soils.

Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter

The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and in situ diffusion devices) that could be applied to retrieve the CAM "dark matter" (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics.

Disturbance by soil mixing decreases microbial richness and supports homogenizing community assembly processes

The spatial heterogeneity of soil's microhabitats warrants the study of ecological patterns and community assembly processes in the context of physical disturbance that disrupts the inherent spatial isolation of soil microhabitats and microbial communities. By mixing soil at various frequencies in a 16-week lab incubation, we explored the effects of physical disturbance on soil bacterial richness, community composition, and community assembly processes. We hypothesized that well-mixed soil would harbor a less rich microbial community, with community assembly marked by homogenizing dispersal and homogeneous selection. Using 16S rRNA gene sequencing, we inferred community assembly processes, estimated richness and differential abundance, and calculated compositional dissimilarity. Findings supported our hypotheses, with > 20% decrease in soil bacterial richness in well-mixed soil. Soil mixing caused communities to diverge from unmixed controls (Bray-Curtis dissimilarity; 0.75 vs. 0.25), while reducing within-group heterogeneity. Our results imply that the vast diversity observed in soil may be supported by spatial heterogeneity and isolation of microbial communities, and also provide insight into the effects of physical disturbance and community coalescence events. By isolating and better understanding the effects of spatial heterogeneity and disconnectivity on soil microbial communities, we can better extrapolate how anthropogenic disturbances may affect broad soil functions.

Hypersymbiotics™: An artistic reflection on the ethical and environmental implications of microbiome research and new technologies

This essay describes my ongoing series "Hypersymbiotics™," which began in 2012 and explores the potential ways in which our microbiome, genetics, epigenetics and even our environment could potentially be enhanced to turn us into human 'super-organisms.' The series includes performances and installations involving BioArt, as well as photographic documentation of ephemeral artworks and takes the form of a vehicle for public discussion about new healthcare technologies. The essay discusses artworks made using synthetic biology techniques including CRISPR genetic modification in bacteria and yeasts, and gene editing in plants, as well as using artificial intelligence and stem cell research. It critiques the role of the media and advertising in the promotion of complex new biomedical technologies. The "Hypersymbiotics™" series is deeply concerned with promoting public understanding of the ethical implications of new scientific developments and enabling reflection and debate. At its core the artwork is about knowledge, power, and control and where that resides.

Environmental structure impacts microbial composition and secondary metabolism

Determining the drivers of microbial community assembly is a central theme of microbial ecology, and chemical ecologists seek to characterize how secondary metabolites mediate these assembly patterns. Environmental structure affects how communities assemble and what metabolic pathways aid in that assembly. Here, we bridged these two perspectives by addressing the chemical drivers of community assembly within a spatially structured landscape with varying oxygen availability. We hypothesized that structured environments would favor higher microbial diversity and metabolite diversity. We anticipated that the production of a compound would be more advantageous in a structured environment (less mixing) compared to an unstructured environment (more mixing), where the molecule would have a diminished local effect. We observed this to be partially true in our experiments: structured environments had similar microbial diversity compared to unstructured environments but differed significantly in the metabolites produced. We also found that structured environments selected for communities with higher evenness, rather than communities with higher richness. This supports the idea that when characterizing the drivers of community assembly, it matters less about who is there and more about what they are doing. Overall, these data contribute to a growing effort to approach microbial community assembly with interdisciplinary tools and perspectives.

Quorum quenching strategy for biofouling control in membrane photobioreactor

This study aims to reduce membrane fouling in membrane photobioreactor (MPBR) through the quorum quenching (QQ) strategy. For this purpose, the QQ beads (immobilized Rhodococcus sp. BH4) were added to the MPBR, and antifouling ability was evaluated in consideration of the changes in transmembrane pressure (TMP), extracellular polymeric substance (EPS), microbial community, and cake layer morphology on the membrane surface. The results showed that the TMP of control MPBR (MPBR-C) reached 818 mbar and 912 mbar on the operation hours of 35 and 170, while the TMP of experimental MPBR (MPBR-QQ) was only 448 mbar and 676 mbar, respectively. The QQ strategy effectively reduced the EPS content in MPBR. The microscopic observations indicated that the QQ diminished the cake layer formation and pore-blocking on the membrane surface. Comparisons of 16S and 18S gene communities revealed minor differences between bacterial and eukaryotic species in MPBRs at phylum and class levels.

Closed microbial communities self-organize to persistently cycle carbon

Life on Earth depends on ecologically driven nutrient cycles to regenerate resources. Understanding how nutrient cycles emerge from a complex web of ecological processes is a central challenge in ecology. However, we lack model ecosystems that can be replicated, manipulated, and quantified in the laboratory, making it challenging to determine how changes in composition and the environment impact cycling. Enabled by a new high-precision method to quantify carbon cycling, we show that materially closed microbial ecosystems (CES) provided with only light self-organize to robustly cycle carbon. Studying replicate CES that support a carbon cycle reveals variable community composition but a conserved set of metabolic capabilities. Our study helps establish CES as model biospheres for studying how ecosystems persistently cycle nutrients.

Cycles of nutrients (N, P, etc.) and resources (C) are a defining emergent feature of ecosystems. Cycling plays a critical role in determining ecosystem structure at all scales, from microbial communities to the entire biosphere. Stable cycles are essential for ecosystem persistence because they allow resources and nutrients to be regenerated. Therefore, a central problem in ecology is understanding how ecosystems are organized to sustain robust cycles. Addressing this problem quantitatively has proved challenging because of the difficulties associated with manipulating ecosystem structure while measuring cycling. We address this problem using closed microbial ecosystems (CES), hermetically sealed microbial consortia provided with only light. We develop a technique for quantifying carbon cycling in hermetically sealed microbial communities and show that CES composed of an alga and diverse bacterial consortia self-organize to robustly cycle carbon for months. Comparing replicates of diverse CES, we find that carbon cycling does not depend strongly on the taxonomy of the bacteria present. Moreover, despite strong taxonomic differences, self-organized CES exhibit a conserved set of metabolic capabilities. Therefore, an emergent carbon cycle enforces metabolic but not taxonomic constraints on ecosystem organization. Our study helps establish closed microbial communities as model ecosystems to study emergent function and persistence in replicate systems while controlling community composition and the environment.

Integrated approach in LDPE degradation - An application using Winogradsky column, computational modeling, and pathway prediction

Plastic pollution in the current scenario requires a sustainable and eco-friendly treatment process. Single-use plastics accumulate more than recyclable plastic wastes. Low-Density Polyethylene (LDPE) is one among the plastic family with inert characteristics. The traditional method, such as landfilling, develops pollution resistant micro-organisms. It is involved in the exploitation of the native microbes to the fullest. The soil of the Kodungaiyur, agriculture site, and Otteri dumpyard were used, which resulted in nearly 22.97 ± 2.7115%, 15.91667 ± 2.73775%, and 10.74 ± 0.502925% of LDPE degradation in 30 days without nutrient supplements. The enrichment of the column by organic nutrients increased the degradation of LDPE. The column enrichment was confirmed by the sulfur oxidizing bacteria (SOB) Escherichia coli and Pseudomonas stutzeri, which produced 195 mg/mL of sulfate ions. The FTIR of the LDPE degradation showed the polymer's oxygenation, while the electron microscopic images revealed cracks. In addition, an attempt was made to fit the experimental time-series data into suitable mathematical models to look at prediction and elementary forecasting. Three mathematical models, namely the customized moving averages model (CMAM), simple liinear regression model (SLRM), and a modified linear regression model (MLRM) with a lag, were able to represent the real experimental data complementarily.

Winogradsky columns as a strategy to study typically rare microbial eukaryotes

Winogradsky columns have been widely used to study soil microbial communities, but the vast majority of those investigations have focused on the ecology and diversity of bacteria. In contrast, microbial eukaryotes (ME) have been regularly overlooked in studies based on experimental soil columns. Despite the recognized ecological relevance of ME in soil communities, investigations focused on ME diversity and the abundance of certain groups of interest are still scarce. In the present study, we used DNA metabarcoding (high-throughput sequencing of the V4 region of the 18S rRNA locus) to survey the ME diversity and abundance in an experimental Winogradsky soil column. Consistent with previous surveys in natural soils, our survey identified members of Cercozoa (Rhizaria; 31.2%), Apicomplexa and Ciliophora (Alveolata; 12.5%) as the predominant ME groups, but at particular depths we also detected the abundant presence of ME lineages that are typically rare in natural environments, such as members of the Vampyrellida (Rhizaria) and Breviatea (Amorphea). Our survey demonstrates that experimental soil columns are an efficient enrichment-culture approach that can enhance investigations about the diversity and ecology of ME in soils.

Non-domestic wastewater treatment with fungal/bacterial consortium followed by Chlorella sp., and thermal conversion of the generated sludge

Liquid waste from biological stains is considered non-domestic wastewater difficult to treat, generating high environmental impact. Therefore, the objective of this work was to carry out secondary and tertiary treatment of these effluents at a pilot scale, using a fungal/bacterial consortium followed by Chorella sp., for 15 days. In addition, to obtain an adsorbent material for Malachite Green dye removal, sludge generated in the plant and pine bark co-pyrolysis was performed. For microalgae isolation and selection of the Chlorophyceae class, Chlorococcales order, and Chorella sp. genus Winogradsky columns were employed. After 15 days of pilot plant treatment, removal percentages of 91 ± 2%, 90 ± 4% and 17 ± 2% were obtained for Colour Units, Chemical Oxygen Demand and Nitrates, respectively. Two types of class II biochar (BC₅₀₀ and BC₇₀₀) and one of class III (BC₃₀₀) were produced. The highest value for Fixed carbon (FC) was obtained at 300 °C (27.3 ± 3%), decreasing as the temperature increased by 25.9 ± 5% and 24.8 ± 2%, for BC₅₀₀ and BC₇₀₀, respectively. Biochar yield was 62.1 ± 3%, 46.3 ± 4% and 31.6 ± 3% for BC₃₀₀, BC₅₀₀ and BC₇₀₀, respectively. Finally, BC₅₀₀ and BC₇₀₀ biochar efficiently adsorbed Malachite Green obtaining qe values of 0.290 ± 0.032, 0.281 ± 0.015, 0.186 ± 0.009 and 0.191 ± 0.012 mg g^-1 at pH values of 4.0 and 8.0 ± 0.2, respectively. Pseudo-second order model demonstrated a chemical adsorption took place, which was influenced by pH.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02780-1.

Implication of Viral Infections for Greenhouse Gas Dynamics in Freshwater Wetlands: Challenges and Perspectives

Viruses are non-living, acellular entities, and the most abundant biological agents on earth. They are widely acknowledged as having the capacity to influence global biogeochemical cycles by infecting the bacterial and archaeal populations that regulate carbon and nutrient turnover. Evidence suggests that the majority of viruses in wetlands are bacteriophages, but despite their importance, studies on how viruses control the prokaryotic community and the concomitant impacts on ecosystem function (such as carbon cycling and greenhouse gas flux) in wetlands are rare. Here we investigate virus-prokaryote interactions in freshwater wetland ecosystems in the context of their potential influence on biogeochemical cycling. Specifically, we (1) synthesize existing literature to establish current understanding of virus-prokaryote interactions, focusing on the implications for wetland greenhouse gas dynamics and (2) identify future research priorities. Viral dynamics in freshwater wetlands have received much less attention compared to those in marine ecosystems. However, based on our literature review, within the last 10 years, viral ecology studies on freshwater wetlands have increased twofold. Despite this increase in literature, the potential implication of viral infections on greenhouse gas emission dynamics is still a knowledge gap. We hypothesize that the rate of greenhouse gas emissions and the pool of sequestered carbon could be strongly linked to the type and rate of viral infection. Viral replication mechanism choice will consequently influence the microbial efficiency of organic matter assimilation and thus the ultimate fate of carbon as a greenhouse gas or stored in soils.

Carbonate Precipitation in Mixed Cyanobacterial Biofilms Forming Freshwater Microbial Tufa

: Mixed cyanobacteria-dominated biofilms, enriched from a tributary of the Mérantaise (France) were used to conduct laboratory experiments in order to understand the relationship between the morphology of carbonate precipitates and the biological activity (e.g., cyanobacterial exopolymeric substances (EPS) production, photosynthetic pH increases). DNA sequencing data showed that the enriched biofilm was composed predominantly of two types of filamentous cyanobacteria that belonged to the Oscillatoriaceae and Phormidiaceae families, respectively. Microscopic analysis also indicated the presence of some coccoid cyanobacteria resembling Gloeocapsa. Analysis of carbonate precipitates in experimental biofilms showed three main morphologies: micro-peloids with different shapes of mesocrystals associated with Oscillatoriaceae filaments and theirs EPS, lamellae of carbonate formed directly on Phormidiaceae filaments, and rhombic sparite crystals wrapped in EPS. All crystals were identified by FT-IR spectroscopy as calcite. Similar structures as those that formed in laboratory conditions were observed in the microbial-tufa deposits collected in the stream. Microscopic and spectroscopic analysis of laboratory and natural samples indicated a close proximity of the cyanobacterial EPS and precipitated carbonates in both. Based on the laboratory experiments, we conclude that the microbial tufa in the stream is in an early stage of formation.

Microbial biospherics: The experimental study of ecosystem function and evolution

Awareness that our planet is a self-supporting biosphere with sunlight as its major source of energy for life has resulted in a long-term historical fascination with the workings of self-supporting ecological systems. However, the studies of such systems have never entered the canon of ecological or evolutionary tools and instead, have led a fringe existence connected to life support system engineering and space travel. We here introduce a framework for a renaissance in biospherics based on the study of matter-closed, energy-open ecosystems at a microbial level (microbial biospherics). Recent progress in genomics, robotics, and sensor technology makes the study of closed systems now much more tractable than in the past, and we argue that the time has come to emancipate the study of closed systems from this fringe context and bring them into a mainstream approach for studying ecosystem processes. By permitting highly replicated long-term studies, especially on predetermined and simplified systems, microbial biospheres offer the opportunity to test and develop strong hypotheses about ecosystem function and the ecological and evolutionary determinants of long-term system failure or persistence. Unlike many sciences, ecosystem ecology has never fully embraced a reductionist approach and has remained focused on the natural world in all its complexity. We argue that a reductionist approach to ecosystem ecology, using microbial biospheres, based on a combination of theory and the replicated study of much simpler self-enclosed microsystems could pay huge dividends.

Biogeochemical gradients and microbial communities in Winogradsky columns established with polluted wetland sediments

A Winogradsky column is a miniature ecosystem established with enriched sediments that can be used to study the relationship between biogeochemical gradients, microbial diversity and pollutant transformation. Biogeochemical processes and microbial communities changed with time and depth in Winogradsky columns incubated with heavy-metal-polluted wetland sediments for 520 days. 16S rRNA surveys were complemented by geochemical analyses, including heavy metal proportioning, to evaluate gradients in the mostly anoxic columns. Oxygen was depleted below the water-sediment interface (WSI), while NH4+, Fe2+, S2- and acetate increased by one order of magnitude at the bottom. Microbial niche differentiation occurred mainly by depth and from the light-exposed surface to the interior of the columns. Chemical gradients resulting from nutrient uptake by algae, and from iron and sulphate reduction mainly drove diversification. Heavy-metal proportioning did not significantly influence microbial diversity as Cu and Zn were immobilised at all depths. Proteobacteria were abundant in the top water and the WSI layers, whereas Firmicutes and Bacteroida dominated down-core. Together with low diversity and richness of communities at the WSI and column bottom, changes in the bacterial community coincided with algal-derived carbon sources and cellulose fermentation, respectively. We expect this study to be the starting point for the use Winogradsky columns to study microbial and geochemical dynamics in polluted sediments.

Assembly of microbial communities in replicate nutrient-cycling model ecosystems follows divergent trajectories, leading to alternate stable states

We studied in detail the reproducibility of community development in replicate nutrient-cycling microbial microcosms that were set up identically and allowed to develop under the same environmental conditions. Multiple replicate closed microcosms were constructed using pond sediment and water, enriched with cellulose and sulphate, and allowed to develop over several months under constant environmental conditions, after which their microbial communities were characterized using 16S rRNA gene sequencing. Our results show that initially similar microbial communities can follow alternative - yet stable - trajectories, diverging in time in a system size-dependent manner. The divergence between replicate communities increased in time and decreased with larger system size. In particular, notable differences emerged in the heterotrophic degrader communities in our microcosms; one group of steady state communities was enriched with Firmicutes, while the other was enriched with Bacteroidetes. The communities dominated by these two phyla also contained distinct populations of sulphate-reducing bacteria. This biomodality in community composition appeared to arise during recovery from a low-diversity state that followed initial cellulose degradation and sulphate reduction.

From grass to gas: microbiome dynamics of grass biomass acidification under mesophilic and thermophilic temperatures

BACKGROUND

Separating acidification and methanogenic steps in anaerobic digestion processes can help to optimize the process and contribute to producing valuable sub-products such as methane, hydrogen and organic acids. However, the full potential of this technology has not been fully explored yet. To assess the underlying fermentation process in more detail, a combination of high-throughput sequencing and proteomics on the acidification step of plant material (grass) at both mesophilic and thermophilic temperatures (37 and 55 °C, respectively) was applied for the first time.

RESULTS

High-strength liquor from acidified grass biomass exhibited a low biodiversity, which differed greatly depending on temperature. It was dominated by Bacteroidetes and Firmicutes at 37 °C, and by Firmicutes and Proteobacteria at 55 °C. At the methane stage, Methanosaeta, Methanomicrobium and Methanosarcina proved to be highly sensitive to environmental changes as their abundance in the seed sludges dropped dramatically after transferring the seed sludges from the respective reactors into the experimental setup. Further, an increase in Actinobacteria coincided with reduced biogas production at the end of the experiment. Over 1700 proteins were quantified from the first cycle of acidification samples using label-free quantitative proteome analysis and searching protein databases. The most abundant proteins included an almost complete set of glycolytic enzymes indicating that the microbial population is basically engaged in the degradation and catabolism of sugars. Differences in protein abundances clearly separated samples into two clusters corresponding to culture temperature. More differentially expressed proteins were found under mesophilic (120) than thermophilic (5) conditions.

CONCLUSION

Our results are the first multi-omics characterisation of a two-stage biogas production system with separated acidification and suggest that screening approaches targeting specific taxa such as Methanosaeta, Methanomicrobium and Methanosarcina could be useful diagnostic tools as indicators of environmental changes such as temperature or oxidative stress or, as in the case of Actinobacteria, they could be used as a proxy of the gas production potential of anaerobic digesters. Metaproteome analyses only detected significant expression differences in mesophilic samples, whereas thermophilic samples showed more stable protein composition with an abundance of chaperones suggesting a role in protein stability under thermal stress.

Post-translational modifications are enriched within protein functional groups important to bacterial adaptation within a deep-sea hydrothermal vent environment

BACKGROUND

Post-translational modification (PTM) of proteins is one important strategy employed by bacteria for environmental adaptation. However, PTM profiles in deep-sea microbes remain largely unexplored.

RESULTS

We provide here insight into PTMs in a hydrothermal vent microbial community through integration of metagenomics and metaproteomics. In total, 2919 unique proteins and 1306 unique PTMs were identified, whereas the latter included acetylation, deamination, hydroxylation, methylation, nitrosylation, oxidation, and phosphorylation. These modifications were unevenly distributed among microbial taxonomic and functional categories. A connection between modification types and particular functions was demonstrated. Interestingly, PTMs differed among the orthologous proteins derived from different bacterial groups. Furthermore, proteomic mapping to the draft genome of a Nitrospirae bacterium revealed novel modifications for proteins that participate in energy metabolism, signal transduction, and inorganic ion transport.

CONCLUSIONS

Our results suggest that PTMs are enriched in specific functions, which would be important for microbial adaptation to extreme conditions of the hydrothermal vent. PTMs in deep-sea are highly diverse and divergent, and much broader investigations are needed to obtain a better understanding of their functional roles.