Bacterial populations active in metabolism of C1 compounds in the sediment of Lake Washington, a freshwater lake

Chytrid fungi infecting Arctic microphytobenthic communities under varying salinity conditions

This study aimed to investigate the presence and diversity of fungal parasites in Arctic coastal microphytobenthic communities. These communities represent a key component in the functioning of Arctic trophic food webs. Fungal parasites, particularly Chytridiomycota (chytrids), play significant roles by controlling microalgal bloom events, impacting genetic diversity, modifying microbial interactions, and accelerating nutrient and energy transfer to higher trophic levels. In the context of rapid Arctic warming and increased glacier meltwater, which significantly affects these communities, we used high-throughput sequencing to explore fungal community composition. Our results show that chytrids dominate fungal communities in Arctic benthic habitats and that the overall fungal diversity is primarily influenced by the salinity gradient. Chytrid representation is positively correlated with the presence of potential benthic diatom (Surirella, Nitzschia, Navicula) and green algae (Ulvophyceae) hosts, while microscopic observations provide further evidence for the presence of active chytrid infections.

A new type of submarine chimneys built of halite

In contrast to the subaquatic sulphide and carbonate chimneys, which are known from Mid Ocean Ridges and abyssal submarine volcanoes, chimneys built of salts have not been described yet. Here we present such halite chimneys as a new form of cold-water smokers in hypersaline environments. The here described structures rise up from the bottom of the Dead Sea and result from the submarine discharge of saturated halite-dissolution brines into the salt lake, which is at halite saturation and holds remarkable chloride excess. At the interface with the lake brine, halite precipitates instantaneously, forming chimneys up to several meters in height. The brines leading to the formation of these chimneys vary in composition, while their generation processes are similar. Fresh groundwater from surrounding aquifers enters the saline lake sediments and considerably leaches halite in the adjacencies of the lake. Simultaneously, it mixes with ancient brines before it emerges from the lake floor. The distinct differences in composition between the Dead Sea and the emerging chimney brines lead to the instantaneous crystallisation of halite and few other mineral phases. The chimney structure result from the buoyancy flow of the chimney brines, which are less dense then the ambient Dead Sea. The chimneys indicate intense cavitation of massive halite bodies in the subsurface of the Dead Sea environment, a process that leads to increasing formation of hazardous sinkholes. Since chimneys are proven in shallow water but may be expected in deeper parts too, they are comfortably mappable by echo-sounding or aerial imaging. They thus provide in the Dead Sea as in any likewise setting a potent predictive tool to locate dangerous subsurface cavitation and hence areas that are at risk of collapse in the near future.

The effects of climate and soil depth on living and dead bacterial communities along a longitudinal gradient in Chile

Soil bacterial communities play a critical role in shaping soil stability and formation, exhibiting a dynamic interaction with local climate and soil depth. We employed an innovative DNA separation method to characterize microbial assemblages in low-biomass environments such as deserts and distinguish between intracellular DNA (iDNA) and extracellular DNA (eDNA) in soils. This approach, combined with analyses of physicochemical properties and co-occurrence networks, investigated soil bacterial communities across four sites representing diverse climatic gradients (i.e., arid, semi-arid, Mediterranean, and humid) along the Chilean Coastal Cordillera. The separation method yielded a distinctive unimodal pattern in the iDNA pool alpha diversity, increasing from arid to semi-arid climates and decreasing in humid environments, highlighting the rapid feedback of the iDNA community to increasing soil moisture. In the arid region, harsh surface conditions restrict bacterial growth, leading to peak iDNA abundance and diversity occurring in slightly deeper layers than the other sites. Our findings confirmed the association between specialist bacteria and ecosystem-functional traits. We observed transitions from Halomonas and Delftia, resistant to extreme arid environments, to Class AD3 and the genus Bradyrhizobium, associated with plants and organic matter in humid environments. The distance-based redundancy analysis (dbRDA) analysis revealed that soil pH and moisture were the key parameters that influenced bacterial community variation. The eDNA community correlated slightly better with the environment than the iDNA community. Soil depth was found to influence the iDNA community significantly but not the eDNA community, which might be related to depth-related metabolic activity. Our investigation into iDNA communities uncovered deterministic community assembly and distinct co-occurrence modules correlated with unique bacterial taxa, thereby showing connections with sites and key environmental factors. The study additionally revealed the effects of climatic gradients and soil depth on living and dead bacterial communities, emphasizing the need to distinguish between iDNA and eDNA pools.

Impacts of eutrophication on microbial community structure in sediment, seawater, and phyllosphere of seagrass ecosystems

Introduction

Seagrass-associated microbial communities play a crucial role in the growth and health of seagrasses. However, like seagrass meadows, seagrass-associated microbial communities are often affected by eutrophication. It remains unclear how eutrophication influences the composition and function of microbial communities associated with different parts of seagrass.

Methods

We employed prokaryotic 16S rRNA gene high-throughput sequencing combining microbial community structure analysis and co-occurrence network analysis to investigate variances in microbial community compositions, potential functions and complexities across sediment, seagrass leaves, and seawater within different eutrophic areas of two adjacent seagrass meadows on Hainan Island, China.

Results

Our results indicated that microbial diversity on seagrass leaves was significantly lower than in sediment but significantly higher than in seawater. Both sediment and phyllosphere microbial diversity showed no significant difference between the highly eutrophic and less eutrophic sites in each lagoon. However, sediment microbial diversity was higher in the more eutrophic lagoon, while phyllosphere microbial diversity was higher in the less eutrophic lagoon. Heavy eutrophication increased the relative abundance of phyllosphere microorganisms potentially involved in anaerobic metabolic processes, while reducing those responsible for beneficial functions like denitrification. The main factor affecting microbial diversity was organic carbon in seawater and sediment, with high organic carbon levels leading to decreased microbial diversity. The co-occurrence network analysis revealed that heavy eutrophication notably reduced the complexity and internal connections of the phyllosphere microbial community in comparison to the sediment and seawater microbial communities. Furthermore, ternary analysis demonstrated that heavy eutrophication diminished the external connections of the phyllosphere microbial community with the sediment and seawater microbial communities.

Conclusion

The pronounced decrease in biodiversity and complexity of the phyllosphere microbial community under eutrophic conditions can lead to greater microbial functional loss, exacerbating seagrass decline. This study emphasizes the significance of phyllosphere microbial communities compared to sediment microbial communities in the conservation and restoration of seagrass meadows under eutrophic conditions.

Reduced greenhouse gas emissions from particulate organic matter degradation in iron-enriched sediments

Iron (Fe) plays an important role in the biogeochemical cycling of carbon and nutrients in aquatic systems. Reactive Fe phases can interact with organic carbon and facilitate the removal of carbon from the biogeochemical cycle; however, this important ecosystem function is often strongly controlled by Fe availability. Due to pollution from lignite mining in the Lusatian province in Northeast Germany, large amounts of iron and sulfate are released into the fluvial-lacustrine system of the Spree River. It was hypothesized that the input of freshly precipitated iron oxyhydroxides from mining areas (e.g., ferrihydrite) alter the biodegradation of particulate organic matter (POM) in downstream lacustrine sediments. To investigate the Fe-dependent degradation of POM, slurries mimicking iron-polluted sediments (85 mg Fe per g, 116 mg Fe per g, and 149 mg Fe per g dry weight) were incubated with plankton or leaf POM under anoxic and oxic headspace conditions, and CO2 and CH4 emissions, water chemistry, and stable isotopes of dissolved inorganic carbon were measured. The experiments revealed that (i) with an increasing Fe content, the CO2 and CH4 emissions were gradually reduced, (ii) CO2 and CH4 production was higher during plankton degradation than during leaf decomposition, and (iii) under oxic conditions, CO2 production was higher and CH4 production was lower when compared to the treatments under anoxic conditions. These findings demonstrate that while benthic mineralization of fresh POM typically releases greenhouse gases into the water column, the availability of iron oxyhydroxides can contribute to reduced greenhouse gas emissions from sediments. This is of considerable relevance for future carbon budgets of similar mining-affected, iron-polluted fluvial-lacustrine river systems.

Microbial remineralization processes during postspring-bloom with excess phosphate available in the northern Baltic Sea

The phosphorus (P) concentration is increasing in parts of the Baltic Sea following the spring bloom. The fate of this excess P-pool is an open question, and here we investigate the role of microbial degradation processes in the excess P assimilation phase. During a 17-day-long mesocosm experiment in the southwest Finnish archipelago, we examined nitrogen, phosphorus, and carbon acquiring extracellular enzyme activities in three size fractions (<0.2, 0.2-3, and >3 µm), bacterial abundance, production, community composition, and its predicted metabolic functions. The mesocosms received carbon (C) and nitrogen (N) amendments individually and in combination (NC) to distinguish between heterotrophic and autotrophic processes. Alkaline phosphatase activity occurred mainly in the dissolved form and likely contributed to the excess phosphate conditions together with grazing. At the beginning of the experiment, peptidolytic and glycolytic enzymes were mostly produced by free-living bacteria. However, by the end of the experiment, the NC-treatment induced a shift in peptidolytic and glycolytic activities and degradation of phosphomonoesters toward the particle-associated fraction, likely as a consequence of higher substrate availability. This would potentially promote retention of nutrients in the surface as opposed to sedimentation, but direct sedimentation measurements are needed to verify this hypothesis.

Response of aerobic anoxygenic phototrophic bacteria to limitation and availability of organic carbon

Aerobic anoxygenic phototrophic (AAP) bacteria are an important component of freshwater bacterioplankton. They can support their heterotrophic metabolism with energy from light, enhancing their growth efficiency. Based on results from cultures, it was hypothesized that photoheterotrophy provides an advantage under carbon limitation and facilitates access to recalcitrant or low-energy carbon sources. However, verification of these hypotheses for natural AAP communities has been lacking. Here, we conducted whole community manipulation experiments and compared the growth of AAP bacteria under carbon limited and with recalcitrant or low-energy carbon sources under dark and light (near-infrared light, λ > 800 nm) conditions to elucidate how they profit from photoheterotrophy. We found that AAP bacteria induce photoheterotrophic metabolism under carbon limitation, but they overcompete heterotrophic bacteria when carbon is available. This effect seems to be driven by physiological responses rather than changes at the community level. Interestingly, recalcitrant (lignin) or low-energy (acetate) carbon sources inhibited the growth of AAP bacteria, especially in light. This unexpected observation may have ecosystem-level consequences as lake browning continues. In general, our findings contribute to the understanding of the dynamics of AAP bacteria in pelagic environments.

16S rRNA gene amplicon sequencing data from an Australian wastewater treatment plant

Amplicon sequencing data of the 16S rRNA (V1-V3) gene from 56 effluent and sediment samples from an Australian wastewater treatment plant are reported. Proteobacteria (3.50%-90.09%), Actinobacteria (0.02%-45.71%), and Cyanobacteria (0.05%-63.73%) were dominant in the effluent. The sediment samples were dominated by Proteobacteria (13.14%-84.83%), Chloroflexi (0.84%-42.52%), and Firmicutes (1.54%-17.21%).

Persistent microbial communities in hyperarid subsurface habitats of the Atacama Desert: Insights from intracellular DNA analysis

Desert environments constitute one of the largest and yet most fragile ecosystems on Earth. Under the absence of regular precipitation, microorganisms are the main ecological component mediating nutrient fluxes by using soil components, like minerals and salts, and atmospheric gases as a source for energy and water. While most of the previous studies on microbial ecology of desert environments have focused on surface environments, little is known about microbial life in deeper sediment layers. Our study is extending the limited knowledge about microbial communities within the deeper subsurface of the hyperarid core of the Atacama Desert. By employing intracellular DNA extraction and subsequent 16S rRNA sequencing of samples collected from a soil pit in the Yungay region of the Atacama Desert, we unveiled a potentially viable microbial subsurface community residing at depths down to 4.20 m. In the upper 80 cm of the playa sediments, microbial communities were dominated by Firmicutes taxa showing a depth-related decrease in biomass correlating with increasing amounts of soluble salts. High salt concentrations are possibly causing microbial colonization to cease in the lower part of the playa sediments between 80 and 200 cm depth. In the underlying alluvial fan deposits, microbial communities reemerge, possibly due to gypsum providing an alternative water source. The discovery of this deeper subsurface community is reshaping our understanding of desert soils, emphasizing the need to consider subsurface environments in future explorations of arid ecosystems.

Microbiome analysis reveals Microcystis blooms endogenously seeded from benthos within wastewater maturation ponds

Toxigenic Microcystis blooms periodically disrupt the stabilization ponds of wastewater treatment plants (WWTPs). Dense proliferations of Microcystis cells within the surface waters (SWs) impede the water treatment process by reducing the treatment efficacy of the latent WWTP microbiome. Further, water quality is reduced when conventional treatment leads to Microcystis cell lysis and the release of intracellular microcystins into the water column. Recurrent seasonal Microcystis blooms cause significant financial burdens for the water industry and predicting their source is vital for bloom management strategies. We investigated the source of recurrent toxigenic Microcystis blooms at Australia's largest lagoon-based municipal WWTP in both sediment core (SC) and SW samples between 2018 and 2020. Bacterial community composition of the SC and SW samples according to 16S rRNA gene amplicon sequencing showed that Microcystis sp. was dominant within SW samples throughout the period and reached peak relative abundances (32%) during the summer. The same Microcystis Amplicon sequence variants were present within the SC and SW samples indicating a potential migratory population that transitions between the sediment water and SWs during bloom formation events. To investigate the potential of the sediment to act as a repository of viable Microcystis cells for recurrent bloom formation, a novel in-vitro bloom model was established featuring sediments and sterilized SW collected from the WWTP. Microcystin-producing Microcystis blooms were established through passive resuspension after 12 weeks of incubation. These results demonstrate the capacity of Microcystis to transition between the sediments and SWs in WWTPs, acting as a perennial inoculum for recurrent blooms.IMPORTANCECyanobacterial blooms are prevalent to wastewater treatment facilities owing to the stable, eutrophic conditions. Cyanobacterial proliferations can disrupt operational procedures through the blocking of filtration apparatus or altering the wastewater treatment plant (WWTP) microbiome, reducing treatment efficiency. Conventional wastewater treatment often results in the lysis of cyanobacterial cells and the release of intracellular toxins which pose a health risk to end users. This research identifies a potential seeding source of recurrent toxigenic cyanobacterial blooms within wastewater treatment facilities. Our results demonstrate the capacity of Microcystis to transition between the sediments and surface waters (SWs) of wastewater treatment ponds enabling water utilities to develop adequate monitoring and management strategies. Further, we developed a novel model to demonstrate benthic recruitment of toxigenic Microcystis under laboratory conditions facilitating future research into the genetic mechanisms behind bloom development.

Fungi increases kelp (Ecklonia radiata) remineralisation and dissolved organic carbon, alkalinity, and dimethylsulfoniopropionate (DMSP) production

Fungi are key players in terrestrial organic matter (OM) degradation, but little is known about their role in marine environments. Here we compared the degradation of kelp (Ecklonia radiata) in mesocosms with and without fungicides over 45 days. The aim was to improve our understanding of the vital role of fungal OM degradation and remineralisation and its relevance to marine biogeochemical cycles (e.g., carbon, nitrogen, sulfur, or volatile sulfur). In the presence of fungi, 68 % of the kelp detritus degraded over 45 days, resulting in the production of 0.6 mol of dissolved organic carbon (DOC), 0.16 mol of dissolved inorganic carbon (DIC), 0.23 mol of total alkalinity (TA), and 0.076 mol of CO2, which was subsequently emitted to the atmosphere. Conversely, when fungi were inhibited, the bacterial community diversity was reduced, and only 25 % of the kelp detritus degraded over 45 days. The application of fungicides resulted in the generation of an excess amount of 1.5 mol of DOC, but we observed only 0.02 mol of DIC, and 0.04 mol of TA per one mole of kelp detritus, accompanied by a CO2 emission of 0.081 mol. In contrast, without fungi, remineralisation of kelp detritus to DIC, TA, dimethyl sulfide (DMS), dimethylsulfoniopropionate (DMSP) and methanethiol (MeSH) was significantly reduced. Fungal kelp remineralisation led to a remarkable 100,000 % increase in DMSP production. The observed substantial changes in sediment chemistry when fungi are inhibited highlight the important biogeochemical role of fungal remineralisation, which likely plays a crucial role in defining coastal biogeochemical cycling, blue carbon sequestration, and thus climate regulation.

Strategies of chemolithoautotrophs adapting to high temperature and extremely acidic conditions in a shallow hydrothermal ecosystem

BACKGROUND

Active hydrothermal vents create extreme conditions characterized by high temperatures, low pH levels, and elevated concentrations of heavy metals and other trace elements. These conditions support unique ecosystems where chemolithoautotrophs serve as primary producers. The steep temperature and pH gradients from the vent mouth to its periphery provide a wide range of microhabitats for these specialized microorganisms. However, their metabolic functions, adaptations in response to these gradients, and coping mechanisms under extreme conditions remain areas of limited knowledge. In this study, we conducted temperature gradient incubations of hydrothermal fluids from moderate (pH = 5.6) and extremely (pH = 2.2) acidic vents. Combining the DNA-stable isotope probing technique and subsequent metagenomics, we identified active chemolithoautotrophs under different temperature and pH conditions and analyzed their specific metabolic mechanisms.

RESULTS

We found that the carbon fixation activities of Nautiliales in vent fluids were significantly increased from 45 to 65 °C under moderately acidic condition, while their heat tolerance was reduced under extremely acidic conditions. In contrast, Campylobacterales actively fixed carbon under both moderately and extremely acidic conditions under 30 - 45 °C. Compared to Campylobacterales, Nautiliales were found to lack the Sox sulfur oxidation system and instead use NAD(H)-linked glutamate dehydrogenase to boost the reverse tricarboxylic acid (rTCA) cycle. Additionally, they exhibit a high genetic potential for high activity of cytochrome bd ubiquinol oxidase in oxygen respiration and hydrogen oxidation at high temperatures. In terms of high-temperature adaption, the rgy gene plays a critical role in Nautiliales by maintaining DNA stability at high temperature. Genes encoding proteins involved in proton export, including the membrane arm subunits of proton-pumping NADH: ubiquinone oxidoreductase, K+ accumulation, selective transport of charged molecules, permease regulation, and formation of the permeability barrier of bacterial outer membranes, play essential roles in enabling Campylobacterales to adapt to extremely acidic conditions.

CONCLUSIONS

Our study provides in-depth insights into how high temperature and low pH impact the metabolic processes of energy and main elements in chemolithoautotrophs living in hydrothermal ecosystems, as well as the mechanisms they use to adapt to the extreme hydrothermal conditions. Video Abstract.

Substrate Specificity of Biofilms Proximate to Historic Shipwrecks

The number of built structures on the seabed, such as shipwrecks, energy platforms, and pipelines, is increasing in coastal and offshore regions. These structures, typically composed of steel or wood, are substrates for microbial attachment and biofilm formation. The success of biofilm growth depends on substrate characteristics and local environmental conditions, though it is unclear which feature is dominant in shaping biofilm microbiomes. The goal of this study was to understand the substrate- and site-specific impacts of built structures on short-term biofilm composition and functional potential. Seafloor experiments were conducted wherein steel and wood surfaces were deployed for four months at distances extending up to 115 m away from three historic (>50 years old) shipwrecks in the Gulf of Mexico. DNA from biofilms on the steel and wood was extracted, and metagenomes were sequenced on an Illumina NextSeq. A bioinformatics analysis revealed that the taxonomic composition was significantly different between substrates and sites, with substrate being the primary determining factor. Regardless of site, the steel biofilms had a higher abundance of genes related to biofilm formation, and sulfur, iron, and nitrogen cycling, while the wood biofilms showed a higher abundance of manganese cycling and methanol oxidation genes. This study demonstrates how substrate composition shapes biofilm microbiomes and suggests that marine biofilms may contribute to nutrient cycling at depth. Analyzing the marine biofilm microbiome provides insight into the ecological impact of anthropogenic structures on the seabed.

A modified isooctane-based DNA extraction method from crude oil

Microbes from oil reservoirs shape petroleum composition through processes such as biodegradation or souring. Such processes are considered economically detrimental and might pose health and safety hazards. It is therefore crucial to understand the composition of a reservoir's microbial community and its metabolic capabilities. However, such analyses are hindered by difficulties in extracting DNA from such complex fluids as crude oil. Here, we present a novel DNA extraction method from oils with a wide American Petroleum Institute (API) gravity (density) range. We investigated the ability to extract cells from oils with different solvents and surfactants, the latter both nonionic and ionic. Furthermore, we evaluated three DNA extraction methods. Overall, the best DNA yields and the highest number of 16S rRNA reads were achieved with isooctane as a solvent, followed by an ionic surfactant treatment using sodium dodecyl sulfate and DNA extraction using the PowerSoil Pro Kit (Qiagen). The final method was then applied to various oils from oil reservoirs collected in aseptic conditions. Despite the expected low cell density of 101-103 cells/ml, the new method yielded reliable results, with average 16S rRNA sequencing reads in the order of 41431 (±8860) per sample. Thermophilic, halophilic, and anaerobic taxa, which are most likely to be indigenous to the oil reservoir, were found in all samples. API gravity and DNA yield, despite the sufficient DNA obtained, did not show a correlation.

Reduced nitrite accumulation at the primary nitrite maximum in the cyclonic eddies in the western North Pacific subtropical gyre

Nitrite, an intermediate product of the oxidation of ammonia to nitrate (nitrification), accumulates in upper oceans, forming the primary nitrite maximum (PNM). Nitrite concentrations in the PNM are relatively low in the western North Pacific subtropical gyre (wNPSG), where eddies are frequent and intense. To explain these low nitrite concentrations, we investigated nitrification in cyclonic eddies in the wNPSG. We detected relatively low half-saturation constants (i.e., high substrate affinities) for ammonia and nitrite oxidation at 150 to 200 meter water depth. Eddy-induced displacement of high-affinity nitrifiers and increased substrate supply enhanced ammonia and nitrite oxidation, depleting ambient substrate concentrations in the euphotic zone. Nitrite oxidation is more strongly enhanced by the cyclonic eddies than ammonia oxidation, reducing concentrations and accelerating the turnover of nitrite in the PNM. These findings demonstrate a spatial decoupling of the two steps of nitrification in response to mesoscale processes and provide insights into physical-ecological controls on the PNM.

An improved method for intracellular DNA (iDNA) recovery from terrestrial environments

The simultaneous extraction of intracellular DNA (iDNA) and extracellular DNA (eDNA) can help to separate the living in situ community (represented by iDNA) from background DNA that originated both from past communities and from allochthonous sources. As iDNA and eDNA extraction protocols require separating cells from the sample matrix, their DNA yields are generally lower than direct methods that lyse the cells within the sample matrix. We, therefore, tested different buffers with and without adding a detergent mix (DM) in the extraction protocol to improve the recovery of iDNA from surface and subsurface samples that covered a variety of terrestrial environments. The combination of a highly concentrated sodium phosphate buffer plus DM significantly improved iDNA recovery for almost all tested samples. Additionally, the combination of sodium phosphate and EDTA improved iDNA recovery in most of the samples and even allowed the successful extraction of iDNA from extremely low-biomass iron-bearing rock samples taken from the deep biosphere. Based on our results, we recommend using a protocol with sodium phosphate in combination with either a DM (NaP 300 mM + DM) or EDTA (NaP + EDTA 300 mM). Furthermore, for studies that rely on the eDNA pool, we recommend using buffers solely based on sodium phosphate because the addition of EDTA or a DM resulted in a decrease in eDNA for most of the tested samples. These improvements can help reduce community bias in environmental studies and contribute to better characterizations of both modern and past ecosystems.

Temperature-Related Short-Term Succession Events of Bacterial Phylotypes in Potter Cove, Antarctica

In recent years, our understanding of the roles of bacterial communities in the Antarctic Ocean has substantially improved. It became evident that Antarctic marine bacteria are metabolically versatile, and even closely related strains may differ in their functionality and, therefore, affect the ecosystem differently. Nevertheless, most studies have been focused on entire bacterial communities, with little attention given to individual taxonomic groups. Antarctic waters are strongly influenced by climate change; thus, it is crucial to understand how changes in environmental conditions, such as changes in water temperature and salinity fluctuations, affect bacterial species in this important area. In this study, we show that an increase in water temperature of 1 °C was enough to alter bacterial communities on a short-term temporal scale. We further show the high intraspecific diversity of Antarctic bacteria and, subsequently, rapid intra-species succession events most likely driven by various temperature-adapted phylotypes. Our results reveal pronounced changes in microbial communities in the Antarctic Ocean driven by a single strong temperature anomaly. This suggests that long-term warming may have profound effects on bacterial community composition and presumably functionality in light of continuous and future climate change.

Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species

Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O₂ (~7%). The cave's surface-water microbial community is dominated by bacteria we identified as Thiovulum. We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum. We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca. T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O₂ and NO₃^- as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.

Bacterial, Archaeal, and Eukaryote Diversity in Planktonic and Sessile Communities Inside an Abandoned and Flooded Iron Mine (Quebec, Canada)

Abandoned and flooded ore mines are examples of hostile environments (cold, dark, oligotrophic, trace metal) with a potential vast diversity of microbial communities rarely characterized. This study aimed to understand the effects of depth, the source of water (surface or groundwater), and abiotic factors on the communities present in the old Forsyth iron mine in Quebec (Canada). Water and biofilm samples from the mine were sampled by a team of technical divers who followed a depth gradient (0 to 183 m deep) to study the planktonic and sessile communities’ diversity and structure. We used 16S/18S rRNA amplicon to characterize the taxonomic diversity of Bacteria, Archaea, and Eukaryotes. Our results show that depth was not a significant factor explaining the difference in community composition observed, but lifestyle (planktonic/sessile) was. We discovered a vast diversity of microbial taxa, with taxa involved in carbon- and sulfur-cycling. Sessile communities seem to be centered on C1-cycling with fungi and heterotrophs likely adapted to heavy-metal stress. Planktonic communities were dominated by ultra-small archaeal and bacterial taxa, highlighting harsh conditions in the mine waters. Microbial source tracking indicated sources of communities from surface to deeper layers and vice versa, suggesting the dispersion of organisms in the mine, although water connectivity remains unknown.

From Recharge, to Groundwater, to Discharge Areas in Aquifer Systems in Quebec (Canada): Shaping of Microbial Diversity and Community Structure by Environmental Factors

Groundwater recharge and discharge rates and zones are important hydrogeological characteristics of aquifer systems, yet their impact on the formation of both subterranean and surface microbiomes remains largely unknown. In this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community of seven different aquifers, including the recharge and discharge areas of each system. The connectivity between subsurface and surface microbiomes was evaluated at each site, and the temporal succession of groundwater microbial communities was further assessed at one of the sites. Bacterial and archaeal community composition varied between the different sites, reflecting different geological characteristics, with communities from unconsolidated aquifers being distinct from those of consolidated aquifers. Our results also revealed very little to no contribution of surface recharge microbial communities to groundwater communities as well as little to no contribution of groundwater microbial communities to surface discharge communities. Temporal succession suggests seasonal shifts in composition for both bacterial and archaeal communities. This study demonstrates the highly diverse communities of prokaryotes living in aquifer systems, including zones of groundwater recharge and discharge, and highlights the need for further temporal studies with higher resolution to better understand the connectivity between surface and subsurface microbiomes.

Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits

Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28 S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments.

Plastic pollution fosters more microbial growth in lakes than natural organic matter

Plastic debris widely pollutes freshwaters. Abiotic and biotic degradation of plastics releases carbon-based substrates that are available for heterotrophic growth, but little is known about how these novel organic compounds influence microbial metabolism. Here we found leachate from plastic shopping bags was chemically distinct and more bioavailable than natural organic matter from 29 Scandinavian lakes. Consequently, plastic leachate increased bacterial biomass acquisition by 2.29-times when added at an environmentally-relevant concentration to lake surface waters. These results were not solely attributable to the amount of dissolved organic carbon provided by the leachate. Bacterial growth was 1.72-times more efficient with plastic leachate because the added carbon was more accessible than natural organic matter. These effects varied with both the availability of alternate, especially labile, carbon sources and bacterial diversity. Together, our results suggest that plastic pollution may stimulate aquatic food webs and highlight where pollution mitigation strategies could be most effective.

Ultra-high resolution mass spectrometry revealed that plastic bags leach labile compounds. Bioassays performed in Scandinavian lakes indicated that these compounds are incorporated into biomass faster and more efficiently than natural organic matter.

Methanol utilizers of the rhizosphere and phyllosphere of a common grass and forb host species

BACKGROUND

Managed grasslands are global sources of atmospheric methanol, which is one of the most abundant volatile organic compounds in the atmosphere and promotes oxidative capacity for tropospheric and stratospheric ozone depletion. The phyllosphere is a favoured habitat of plant-colonizing methanol-utilizing bacteria. These bacteria also occur in the rhizosphere, but their relevance for methanol consumption and ecosystem fluxes is unclear. Methanol utilizers of the plant-associated microbiota are key for the mitigation of methanol emission through consumption. However, information about grassland plant microbiota members, their biodiversity and metabolic traits, and thus key actors in the global methanol budget is largely lacking.

RESULTS

We investigated the methanol utilization and consumption potentials of two common plant species (Festuca arundinacea and Taraxacum officinale) in a temperate grassland. The selected grassland exhibited methanol formation. The detection of ¹³C derived from ¹³C-methanol in 16S rRNA of the plant microbiota by stable isotope probing (SIP) revealed distinct methanol utilizer communities in the phyllosphere, roots and rhizosphere but not between plant host species. The phyllosphere was colonized by members of Gamma- and Betaproteobacteria. In the rhizosphere, ¹³C-labelled Bacteria were affiliated with Deltaproteobacteria, Gemmatimonadates, and Verrucomicrobiae. Less-abundant ¹³C-labelled Bacteria were affiliated with well-known methylotrophs of Alpha-, Gamma-, and Betaproteobacteria. Additional metagenome analyses of both plants were consistent with the SIP results and revealed Bacteria with methanol dehydrogenases (e.g., MxaF1 and XoxF1-5) of known but also unusual genera (i.e., Methylomirabilis, Methylooceanibacter, Gemmatimonas, Verminephrobacter). ¹⁴C-methanol tracing of alive plant material revealed divergent potential methanol consumption rates in both plant species but similarly high rates in the rhizosphere and phyllosphere.

CONCLUSIONS

Our study revealed the rhizosphere as an overlooked hotspot for methanol consumption in temperate grasslands. We further identified unusual new but potentially relevant methanol utilizers besides well-known methylotrophs in the phyllosphere and rhizosphere. We did not observe a plant host-specific methanol utilizer community. Our results suggest that our approach using quantitative SIP and metagenomics may be useful in future field studies to link gross methanol consumption rates with the rhizosphere and phyllosphere microbiome.

Photoheterotrophy by aerobic anoxygenic bacteria modulates carbon fluxes in a freshwater lake

Lakes are a significant component of the global carbon cycle. Respiration exceeds net primary production in most freshwater lakes, making them a source of CO₂ to the atmosphere. Driven by heterotrophic microorganisms, respiration is assumed to be unaffected by light, thus it is measured in the dark. However, photoheterotrophs, such as aerobic anoxygenic photoheterotrophic (AAP) bacteria that produce ATP via photochemical reactions, substantially reduce respiration in the light. They are an abundant and active component of bacterioplankton, but their photoheterotrophic contribution to microbial community metabolism remains unquantified. We showed that the community respiration rate in a freshwater lake was reduced by 15.2% (95% confidence interval (CI): 6.6-23.8%) in infrared light that is usable by AAP bacteria but not by primary producers. Moreover, significantly higher assimilation rates of glucose (18.1%; 7.8-28.4%), pyruvate (9.5%; 4.2-14.8%), and leucine (5.9%; 0.1-11.6%) were measured in infrared light. At the ecosystem scale, the amount of CO₂ from respiration unbalanced by net primary production was by 3.69 × 10⁹ g CO₂ lower over these two sampling seasons when measured in the infrared light. Our results demonstrate that dark measurements of microbial activity significantly bias the carbon fluxes, providing a new paradigm for their quantification in aquatic environments.

DNA-SIP reveals an overlooked methanotroph, Crenothrix sp., involved in methane consumption in shallow lake sediments

Methanotrophs are the main consumers of methane produced in lake sediments. In shallow lakes suffering from eutrophication, methanogenesis is accelerated by the excess organic carbon input, and thus methanotrophs play a key role in regulating this methane flux as well as carbon cycling. Here, we applied nucleic acid stable isotope probing (SIP) to investigate the active methanotrophic microbial community in sediments of several shallow lakes affected by eutrophication. Our results showed that an active methanotrophic community dominated by gamma-proteobacterial methanotrophs, as well as abundant beta-proteobacterial methanol-utilizers, was involved in methane-derived carbon assimilation. Crenothrix, a filamentous methanotroph, was found to be a key methane consumer in all studied lakes. The ecological role of Crenothrix in lacustrine ecosystems is so far poorly understood, with only limited information on its existence in the water column of stratified lakes. Our results provide a novel ecological insight into this group by revealing a wide distribution of Crenothrix in lake sediments. The active methane assimilation by Crenothrix also suggested that it might represent a so far overlooked but crucial biological sink of methane in shallow lakes.

Antarctic Glacial Meltwater Impacts the Diversity of Fungal Parasites Associated With Benthic Diatoms in Shallow Coastal Zones

Aquatic ecosystems are frequently overlooked as fungal habitats, although there is increasing evidence that their diversity and ecological importance are greater than previously considered. Aquatic fungi are critical and abundant components of nutrient cycling and food web dynamics, e.g., exerting top-down control on phytoplankton communities and forming symbioses with many marine microorganisms. However, their relevance for microphytobenthic communities is almost unexplored. In the light of global warming, polar regions face extreme changes in abiotic factors with a severe impact on biodiversity and ecosystem functioning. Therefore, this study aimed to describe, for the first time, fungal diversity in Antarctic benthic habitats along the salinity gradient and to determine the co-occurrence of fungal parasites with their algal hosts, which were dominated by benthic diatoms. Our results reveal that Ascomycota and Chytridiomycota are the most abundant fungal taxa in these habitats. We show that also in Antarctic waters, salinity has a major impact on shaping not just fungal but rather the whole eukaryotic community composition, with a diversity of aquatic fungi increasing as salinity decreases. Moreover, we determined correlations between putative fungal parasites and potential benthic diatom hosts, highlighting the need for further systematic analysis of fungal diversity along with studies on taxonomy and ecological roles of Chytridiomycota.

Land-use type temporarily affects active pond community structure but not gene expression patterns

Changes in land use and agricultural intensification threaten biodiversity and ecosystem functioning of small water bodies. We studied 67 kettle holes (KH) in an agricultural landscape in northeastern Germany using landscape-scale metatranscriptomics, to understand the responses of active bacterial, archaeal, and eukaryotic communities, to land-use type. These KH are proxies of the millions of small standing water bodies of glacial origin spread across the northern hemisphere. Like other landscapes in Europe, the study area has been used for intensive agriculture since the 1950s. In contrast to a parallel eDNA study which revealed the homogenization of biodiversity across KH conceivably resulting from long-lasting intensive agriculture, land-use type affected the structure of the active KH communities during spring crop fertilization, but not a month later. This effect was more pronounced in eukaryotes than in bacteria. In contrast, gene expression patterns did not differ between months or across land-use type, suggesting a high degree of functional redundancy across the KH communities. Variability in gene expression was best explained by active bacterial and eukaryotic community structures, suggesting that these changes in functioning are primarily driven by interactions between organisms. Our results show that influences of the surrounding landscape result in temporary changes in the activity of different community members. Thus, even in KH where biodiversity has been homogenized, communities continue to respond to land management. This needs to be considered when developing sustainable management options for restoration purposes and for successful mitigation of further biodiversity loss in agricultural landscapes.

Lineage-Specific Growth Curves Document Large Differences in Response of Individual Groups of Marine Bacteria to the Top-Down and Bottom-Up Controls

Marine bacterioplankton represent a diverse assembly of species differing largely in their abundance, physiology, metabolic activity, and role in microbial food webs. To analyze their sensitivity to bottom-up and top-down controls, we performed a manipulation experiment where grazers were removed, with or without the addition of phosphate. Using amplicon-reads normalization by internal standard (ARNIS), we reconstructed growth curves for almost 300 individual phylotypes. Grazer removal caused a rapid growth of most bacterial groups, which grew at rates of 0.6 to 3.5 day⁻¹, with the highest rates (>4 day⁻¹) recorded among Rhodobacteraceae, Oceanospirillales, Alteromonadaceae, and Arcobacteraceae. Based on their growth response, the phylotypes were divided into three basic groups. Most of the phylotypes responded positively to both grazer removal as well as phosphate addition. The second group (containing, e.g., Rhodobacterales and Rhizobiales) responded to the grazer removal but not to the phosphate addition. Finally, some clades, such as SAR11 and Flavobacteriaceae, responded only to phosphate amendment but not to grazer removal. Our results show large differences in bacterial responses to experimental manipulations at the phylotype level and document different life strategies of marine bacterioplankton. In addition, growth curves of 130 phylogroups of aerobic anoxygenic phototrophs were reconstructed based on changes of the functional pufM gene. The use of functional genes together with rRNA genes may significantly expand the scientific potential of the ARNIS technique.

IMPORTANCE Growth is one of the main manifestations of life. It is assumed generally that bacterial growth is constrained mostly by nutrient availability (bottom-up control) and grazing (top-down control). Since marine bacteria represent a very diverse assembly of species with different metabolic properties, their growth characteristics also largely differ accordingly. Currently, the growth of marine microorganisms is typically evaluated using microscopy in combination with fluorescence in situ hybridization (FISH). However, these laborious techniques are limited in their throughput and taxonomical resolution. Therefore, we combined a classical manipulation experiment with next-generation sequencing to resolve the growth dynamics of almost 300 bacterial phylogroups in the coastal Adriatic Sea. The analysis documented that most of the phylogroups responded positively to both grazer removal and phosphate addition. We observed significant differences in growth kinetics among closely related species, which could not be distinguished by the classical FISH technique.

Oxic and Anoxic Organic Polymer Degradation Potential of Endophytic Fungi From the Marine Macroalga, Ecklonia radiata

Cellulose and chitin are the most abundant polymeric, organic carbon source globally. Thus, microbes degrading these polymers significantly influence global carbon cycling and greenhouse gas production. Fungi are recognized as important for cellulose decomposition in terrestrial environments, but are far less studied in marine environments, where bacterial organic matter degradation pathways tend to receive more attention. In this study, we investigated the potential of fungi to degrade kelp detritus, which is a major source of cellulose in marine systems. Given that kelp detritus can be transported considerable distances in the marine environment, we were specifically interested in the capability of endophytic fungi, which are transported with detritus, to ultimately contribute to kelp detritus degradation. We isolated 10 species and two strains of endophytic fungi from the kelp Ecklonia radiata. We then used a dye decolorization assay to assess their ability to degrade organic polymers (lignin, cellulose, and hemicellulose) under both oxic and anoxic conditions and compared their degradation ability with common terrestrial fungi. Under oxic conditions, there was evidence that Ascomycota isolates produced cellulose-degrading extracellular enzymes (associated with manganese peroxidase and sulfur-containing lignin peroxidase), while Mucoromycota isolates appeared to produce both lignin and cellulose-degrading extracellular enzymes, and all Basidiomycota isolates produced lignin-degrading enzymes (associated with laccase and lignin peroxidase). Under anoxic conditions, only three kelp endophytes degraded cellulose. We concluded that kelp fungal endophytes can contribute to cellulose degradation in both oxic and anoxic environments. Thus, endophytic kelp fungi may play a significant role in marine carbon cycling via polymeric organic matter degradation.

RNA stable isotope probing and high-throughput sequencing to identify active microbial community members in a methane-driven denitrifying biofilm

AIMS

Aerobic methane oxidation coupled to denitrification (AME-D) is a promising process for removing nitrate from groundwater and yet its microbial mechanism and ecological implications are not fully understood. This study used RNA stable isotope probing (RNA-SIP) and high-throughput sequencing to identify the micro-organisms that are actively involved in aerobic methane oxidation within a denitrifying biofilm.

METHODS AND RESULTS

Two RNA-SIP experiments were conducted to investigate labelling of RNA and methane monooxygenase (pmoA) transcripts when exposed to ¹³ C-labelled methane over a 96-hour time period and to determine active bacteria involved in methane oxidation in a denitrifying biofilm. A third experiment was performed to ascertain the extent of ¹³ C labelling of RNA using isotope ratio mass spectrometry (IRMS). All experiments used biofilm from an established packed bed reactor. IRMS confirmed ¹³ C enrichment of the RNA. The RNA-SIP experiments confirmed selective enrichment by the shift of pmoA transcripts into heavier fractions over time. Finally, high-throughput sequencing identified the active micro-organisms enriched with ¹³ C.

CONCLUSIONS

Methanotrophs (Methylovulum spp. and Methylocystis spp.), methylotrophs (Methylotenera spp.) and denitrifiers (Hyphomicrobium spp.) were actively involved in AME-D.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study to use RNA-SIP and high-throughput sequencing to determine the bacteria active within an AME-D community.

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.

Characterizing the "fungal shunt": Parasitic fungi on diatoms affect carbon flow and bacterial communities in aquatic microbial food webs

Microbial interactions in aquatic environments profoundly affect global biogeochemical cycles, but the role of microparasites has been largely overlooked. Using a model pathosystem, we studied hitherto cryptic interactions between microparasitic fungi (chytrid Rhizophydiales), their diatom host Asterionella, and cell-associated and free-living bacteria. We analyzed the effect of fungal infections on microbial abundances, bacterial taxonomy, cell-to-cell carbon transfer, and cell-specific nitrate-based growth using microscopy (e.g., fluorescence in situ hybridization), 16S rRNA gene amplicon sequencing, and secondary ion mass spectrometry. Bacterial abundances were 2 to 4 times higher on individual fungal-infected diatoms compared to healthy diatoms, particularly involving Burkholderiales. Furthermore, taxonomic compositions of both diatom-associated and free-living bacteria were significantly different between noninfected and fungal-infected cocultures. The fungal microparasite, including diatom-associated sporangia and free-swimming zoospores, derived ∼100% of their carbon content from the diatom. By comparison, transfer efficiencies of photosynthetic carbon were lower to diatom-associated bacteria (67 to 98%), with a high cell-to-cell variability, and even lower to free-living bacteria (32%). Likewise, nitrate-based growth for the diatom and fungi was synchronized and faster than for diatom-associated and free-living bacteria. In a natural lacustrine system, where infection prevalence reached 54%, we calculated that 20% of the total diatom-derived photosynthetic carbon was shunted to the parasitic fungi, which can be grazed by zooplankton, thereby accelerating carbon transfer to higher trophic levels and bypassing the microbial loop. The herein termed "fungal shunt" can thus significantly modify the fate of photosynthetic carbon and the nature of phytoplankton-bacteria interactions, with implications for diverse pelagic food webs and global biogeochemical cycles.

Zooplankton carcasses stimulate microbial turnover of allochthonous particulate organic matter

Carbon turnover in aquatic environments is dependent on biochemical properties of organic matter (OM) and its degradability by the surrounding microbial community. Non-additive interactive effects represent a mechanism where the degradation of biochemically persistent OM is stimulated by the provision of bioavailable OM to the degrading microbial community. Whilst this is well established in terrestrial systems, whether it occurs in aquatic ecosystems remains subject to debate. We hypothesised that OM from zooplankton carcasses can stimulate the degradation of biochemically persistent leaf material, and that this effect is influenced by the daphnia:leaf OM ratio and the complexity of the degrading microbial community. Fresh Daphnia magna carcasses and 13C-labelled maize leaves (Zea mays) were incubated at different ratios (1:1, 1:3 and 1:5) alongside either a complex microbial community (<50 µm) or solely bacteria (<0.8 µm). 13C stable-isotope measurements of CO2 analyses were combined with phospholipid fatty acids (PLFA) analysis and DNA sequencing to link metabolic activities, biomass and taxonomic composition of the microbial community. Our experiments indicated a significantly higher respiration of leaf-derived C when daphnia-derived OM was most abundant (i.e. daphnia:leaf OM ratio of 1:1). This process was stronger in a complex microbial community, including eukaryotic microorganisms, than a solely bacterial community. We concluded that non-additive interactive effects were a function of increased C-N chemodiversity and microbial complexity, with the highest net respiration to be expected when chemodiversity is high and the degrading community complex. This study indicates that identifying the interactions and processes of OM degradation is one important key for a deeper understanding of aquatic and thus global carbon cycle.

Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession

Small lakes and ponds occupy an enormous surface area of inland freshwater and represent an important terrestrial-water interface. Disturbances caused by extreme weather events can have substantial effects on these ecosystems. Here, we analysed the dynamics of nutrients and the entire plankton community in two flood events and afterwards, when quasi-stable conditions were established, to investigate the effect of such disturbances on a small forest pond. We show that floodings result in repeated washout of resident organisms and hundredfold increases in nutrient load. Despite this, the microbial community recovers to a predisturbance state within two weeks of flooding through four well-defined succession phases. Reassembly of phytoplankton and especially zooplankton takes up to two times longer and features repetitive and adaptive patterns. Release of dissolved nutrients from the pond is associated with inflow rates and community recovery, and returns to predisturbance levels before microbial compositions recover. Our findings shed light on the mechanisms underlying functional resilience of small waterbodies and are relevant to global change-induced increases in weather extremes.

Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems

Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain approximately 300 different chromosomes with allelic diversity far exceeding that typically harbored by single bacteria genera. Surveying all publicly available sediment sequence archives, we show that Achromatium is common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Although saline and freshwater Achromatium spp. appear phylogenetically separated, the genus Achromatium contains a globally identical, complete functional inventory regardless of habitat. Achromatium spp. cells from differing ecosystems (e.g., from freshwater to saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest that environmental adaptation occurs by increasing the copy number of relevant genes across the cell's hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium and its genomic features reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.

Effects of Thermal Stress on the Gut Microbiome of Juvenile Milkfish (Chanos chanos)

Milkfish, an important aquaculture species in Asian countries, are traditionally cultured in outdoor-based systems. There, they experience potentially stressful fluctuations in environmental conditions, such as temperature, eliciting changes in fish physiology. While the importance of the gut microbiome for the welfare and performance of fish has been recognized, little is known about the effects of thermal stress on the gut microbiome of milkfish and its interactions with the host’s metabolism. We investigated the gut microbiome of juvenile milkfish in a thermal stress experiment, comparing control (26 °C) and elevated temperature (33 °C) treatments over three weeks, analyzing physiological biomarkers, gut microbiome composition, and tank water microbial communities using 16S amplicon sequencing. The gut microbiome was distinct from the tank water and dominated by Cetobacterium, Enterovibrio, and Vibrio. We observed a parallel succession in both temperature treatments, with microbial communities at 33 °C differing more strongly from the control after the initial temperature increase and becoming more similar towards the end of the experiment. As proxy for the fish’s energy status, HSI (hepatosomatic index) was correlated with gut microbiome composition. Our study showed that thermal stress induced changes in the milkfish gut microbiome, which may contribute to the host’s habituation to elevated temperatures over time.

Evidence for signatures of ancient microbial life in paleosols

Loess-paleosol sequences are terrestrial archives of past climate change. They may host traces of ancient microbial life, but little information is available on the recovery of microbial biomarkers from such deposits. We hypothesized that microbial communities in soil horizons up to an age of 127 kyr carry information related to past environments. We extracted DNA from a loess-paleosol sequence near Toshan, Northern Iran, with 26 m thick deposits showing different degrees of soil development, performed quantitative PCR and 16S rRNA gene amplicon sequencing. Periods of soil formation archived within the loess sediment led to higher diversity and bacterial abundance in the paleosol horizons. Community composition fluctuated over the loess-paleosol sequence and was mainly correlated with age and depth, (ADONIS R² < 0.14, P ≤ 0.002), while responses to paleosol soil traits were weaker. Phyla like Bacteriodetes, Proteobacteria or Acidobacteria were more prevalent in paleosol horizons characterized by intense soil formation, while weakly developed paleosols or loess horizons hosted a higher percentage and diversity of Actinobacteria. Taken together, our findings indicate that the microbial community in loess-paleosol sequences carries signatures of earlier environmental conditions that are preserved until today.

Impacts of Extreme Weather Events on Bacterial Community Composition of a Temperate Humic Lake

Extreme weather events are projected to increase in frequency and intensity as climate change continues. Heterotrophic bacteria play a critical role in lake ecosystems, yet little research has been done to determine how they are affected by such extremes. The purpose of this study was to use high-throughput sequencing to explore the bacterial community composition of a humic oligotrophic lake on the North Atlantic Irish coast and to assess the impacts on composition dynamics related to extreme weather events. Samples for sequencing were collected from Lough Feeagh on a fortnightly basis from April to November 2018. Filtration was used to separate free-living and particle-associated bacterial communities and amplicon sequencing was performed for the 16S rRNA V4 region. Two named storms, six high discharge events, and one drought period occurred during the sampling period. These events had variable, context-dependent effects on bacterial communities in Lough Feeagh. The particle-associated community was found to be more likely to respond to physical changes, such as mixing, while the free-living population responded to changes in nutrient and carbon concentrations. Generally, however, the high stability of the bacterial community observed in Lough Feeagh suggests that the bacterial community is relatively resilient to extreme weather events.

Structure and co-occurrence patterns of bacterial communities associated with white faeces disease outbreaks in Pacific white-leg shrimp Penaeus vannamei aquaculture

Bacterial diseases cause production failures in shrimp aquacultures. To understand environmental conditions and bacterial community dynamics contributing to white faeces disease (WFD) events, we analysed water quality and compared bacterial communities in water as well as in intestines and faeces of healthy and diseased shrimps, respectively, via 16S rRNA gene sequencing and qPCR of transmembrane regulatory protein (toxR), thermolabile haemolysin (tlh), and thermostable direct haemolysin genes of pathogenic Vibrio parahaemolyticus as a proxy for virulence. WFD occurred when pH decreased to 7.71–7.84, and Alteromonas, Pseudoalteromonas and Vibrio dominated the aquatic bacterial communities. The disease severity further correlated with increased proportions of Alteromonas, Photobacterium, Pseudoalteromonas and Vibrio in shrimp faeces. These opportunistic pathogenic bacteria constituted up to 60% and 80% of the sequences in samples from the early and advances stages of the disease outbreak, respectively, and exhibited a high degree of co-occurrence. Furthermore, toxR and tlh were detected in water at the disease event only. Notably, bacterial community resilience in water occurred when pH was adjusted to 8. Then WFD ceased without a mortality event. In conclusion, pH was a reliable indicator of the WFD outbreak risk. Dissolved oxygen and compositions of water and intestinal bacteria may also serve as indicators for better prevention of WFD events.

Light and Primary Production Shape Bacterial Activity and Community Composition of Aerobic Anoxygenic Phototrophic Bacteria in a Microcosm Experiment

Phytoplankton is a key component of aquatic microbial communities, and metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon (DOC). Yet, the impact of primary production on bacterial activity and community composition remains largely unknown, as, for example, in the case of aerobic anoxygenic phototrophic (AAP) bacteria that utilize both phytoplankton-derived DOC and light as energy sources. Here, we studied how reduction of primary production in a natural freshwater community affects the bacterial community composition and its activity, focusing primarily on AAP bacteria. The bacterial respiration rate was the lowest when photosynthesis was reduced by direct inhibition of photosystem II and the highest in ambient light condition with no photosynthesis inhibition, suggesting that it was limited by carbon availability. However, bacterial assimilation rates of leucine and glucose were unaffected, indicating that increased bacterial growth efficiency (e.g., due to photoheterotrophy) can help to maintain overall bacterial production when low primary production limits DOC availability. Bacterial community composition was tightly linked to light intensity, mainly due to the increased relative abundance of light-dependent AAP bacteria. This notion shows that changes in bacterial community composition are not necessarily reflected by changes in bacterial production or growth and vice versa. Moreover, we demonstrated for the first time that light can directly affect bacterial community composition, a topic which has been neglected in studies of phytoplankton-bacteria interactions.IMPORTANCE Metabolic coupling between phytoplankton and bacteria determines the fate of dissolved organic carbon in aquatic environments, and yet how changes in the rate of primary production affect the bacterial activity and community composition remains understudied. Here, we experimentally limited the rate of primary production either by lowering light intensity or by adding a photosynthesis inhibitor. The induced decrease had a greater influence on bacterial respiration than on bacterial production and growth rate, especially at an optimal light intensity. This suggests that changes in primary production drive bacterial activity, but the effect on carbon flow may be mitigated by increased bacterial growth efficiencies, especially of light-dependent AAP bacteria. Bacterial activities were independent of changes in bacterial community composition, which were driven by light availability and AAP bacteria. This direct effect of light on composition of bacterial communities has not been documented previously.

Microbial community composition across a coastal hydrological system affected by submarine groundwater discharge (SGD)

Mobile Bay, the fourth largest estuary in the USA located in the northern Gulf of Mexico, is known for extreme hypoxia in the water column during dry season caused by NH4+-rich and anoxic submarine groundwater discharge (SGD). Nutrient dynamics in the coastal ecosystem point to potentially elevated microbial activities; however, little is known about microbial community composition and their functional roles in this area. In this study, we investigated microbial community composition, distribution, and metabolic prediction along the coastal hydrological compartment of Mobile Bay using 16S rRNA gene sequencing. We collected microbial samples from surface (river and bay water) and subsurface water (groundwater and coastal pore water from two SGD sites with peat and sandy lithology, respectively). Salinity was identified as the primary factor affecting the distribution of microbial communities across surface water samples, while DON and PO43- were the major predictor of community shift within subsurface water samples. Higher microbial diversity was found in coastal pore water in comparison to surface water samples. Gammaproteobacteria, Bacteroidia, and Oxyphotobacteria dominated the bacterial community. Among the archaea, methanogens were prevalent in the peat-dominated SGD site, while the sandy SGD site was characterized by a higher proportion of ammonia-oxidizing archaea. Cyanobium PCC-6307 and unclassified Thermodesulfovibrionia were identified as dominant taxa strongly associated with trends in environmental parameters in surface and subsurface samples, respectively. Microbial communities found in the groundwater and peat layer consisted of taxa known for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This finding suggested that microbial communities might also play a significant role in mediating nitrogen transformation in the SGD flow path and in affecting the chemical composition of SGD discharging to the water column. Given the ecological importance of microorganisms, further studies at higher taxonomic and functional resolution are needed to accurately predict chemical biotransformation processes along the coastal hydrological continuum, which influence water quality and environmental condition in Mobile Bay.

Bacterial and Eukaryotic Small-Subunit Amplicon Data Do Not Provide a Quantitative Picture of Microbial Communities, but They Are Reliable in the Context of Ecological Interpretations

High-throughput sequencing (HTS) of amplified fragments of rRNA genes provides unprecedented insight into the diversity of prokaryotic and eukaryotic microorganisms. Unfortunately, HTS data are prone to quantitative biases, which may lead to an erroneous picture of microbial community composition and thwart efforts to advance its understanding. These concerns motivated us to investigate how accurately HTS data characterize the variability of microbial communities, the relative abundances of specific phylotypes, and their relationships with environmental factors in comparison to an established microscopy-based method. We compared results obtained by HTS and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) from three independent aquatic time series for both prokaryotic and eukaryotic microorganisms (almost 900 data points, the largest obtained with both methods so far). HTS and CARD-FISH data disagree with regard to relative abundances of bacterial and eukaryotic phylotypes but identify similar environmental drivers shaping bacterial and eukaryotic communities.

High-throughput sequencing (HTS) of gene amplicons is a preferred method of assessing microbial community composition, because it rapidly provides information from a large number of samples at high taxonomic resolution and low costs. However, mock community studies show that HTS data poorly reflect the actual relative abundances of individual phylotypes, casting doubt on the reliability of subsequent statistical analysis and data interpretation. We investigated how accurately HTS data reflect the variability of bacterial and eukaryotic community composition and their relationship with environmental factors in natural samples. For this, we compared results of HTS from three independent aquatic time series (n = 883) with those from an established, quantitative microscopic method (catalyzed reporter deposition-fluorescence in situ hybridization [CARD-FISH]). Relative abundances obtained by CARD-FISH and HTS disagreed for most bacterial and eukaryotic phylotypes. Nevertheless, the two methods identified the same environmental drivers to shape bacterial and eukaryotic communities. Our results show that amplicon data do provide reliable information for their ecological interpretations. Yet, when studying specific phylogenetic groups, it is advisable to combine HTS with quantification using microscopy and/or the addition of internal standards.

IMPORTANCE High-throughput sequencing (HTS) of amplified fragments of rRNA genes provides unprecedented insight into the diversity of prokaryotic and eukaryotic microorganisms. Unfortunately, HTS data are prone to quantitative biases, which may lead to an erroneous picture of microbial community composition and thwart efforts to advance its understanding. These concerns motivated us to investigate how accurately HTS data characterize the variability of microbial communities, the relative abundances of specific phylotypes, and their relationships with environmental factors in comparison to an established microscopy-based method. We compared results obtained by HTS and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) from three independent aquatic time series for both prokaryotic and eukaryotic microorganisms (almost 900 data points, the largest obtained with both methods so far). HTS and CARD-FISH data disagree with regard to relative abundances of bacterial and eukaryotic phylotypes but identify similar environmental drivers shaping bacterial and eukaryotic communities.

Methane oxidation and methylotroph population dynamics in groundwater mesocosms

Extraction of natural gas from unconventional hydrocarbon reservoirs by hydraulic fracturing raises concerns about methane migration into groundwater. Microbial methane oxidation can be a significant methane sink. Here, we inoculated replicated, sand‐packed, continuous mesocosms with groundwater from a field methane release experiment. The mesocosms experienced thirty‐five weeks of dynamic methane, oxygen and nitrate concentrations. We determined concentrations and stable isotope signatures of methane, carbon dioxide and nitrate and monitored microbial community composition of suspended and attached biomass. Methane oxidation was strictly dependent on oxygen availability and led to enrichment of ¹³C in residual methane. Nitrate did not enhance methane oxidation under oxygen limitation. Methylotrophs persisted for weeks in the absence of methane, making them a powerful marker for active as well as past methane leaks. Thirty‐nine distinct populations of methylotrophic bacteria were observed. Methylotrophs mainly occurred attached to sediment particles. Abundances of methanotrophs and other methylotrophs were roughly similar across all samples, pointing at transfer of metabolites from the former to the latter. Two populations of Gracilibacteria (Candidate Phyla Radiation) displayed successive blooms, potentially triggered by a period of methane famine. This study will guide interpretation of future field studies and provides increased understanding of methylotroph ecophysiology.

Aquatic and terrestrial cyanobacteria produce methane

Evidence is accumulating to challenge the paradigm that biogenic methanogenesis, considered a strictly anaerobic process, is exclusive to archaea. We demonstrate that cyanobacteria living in marine, freshwater, and terrestrial environments produce methane at substantial rates under light, dark, oxic, and anoxic conditions, linking methane production with light-driven primary productivity in a globally relevant and ancient group of photoautotrophs. Methane production, attributed to cyanobacteria using stable isotope labeling techniques, was enhanced during oxygenic photosynthesis. We suggest that the formation of methane by cyanobacteria contributes to methane accumulation in oxygen-saturated marine and limnic surface waters. In these environments, frequent cyanobacterial blooms are predicted to further increase because of global warming potentially having a direct positive feedback on climate change. We conclude that this newly identified source contributes to the current natural methane budget and most likely has been producing methane since cyanobacteria first evolved on Earth.

Diel changes and diversity of pufM expression in freshwater communities of anoxygenic phototrophic bacteria

The anoxygenic phototrophic bacteria (APB) are an active component of aquatic microbial communities. While DNA-based studies have delivered a detailed picture of APB diversity, they cannot provide any information on the activity of individual species. Therefore, we focused on the expression of a photosynthetic gene by APB communities in two freshwater lakes (Cep lake and the Římov Reservoir) in the Czech Republic. First, we analyzed expression levels of pufM during the diel cycle using RT-qPCR. The transcription underwent a strong diel cycle and was inhibited during the day in both lakes. Then, we compared DNA- (total) and RNA-based (active) community composition by sequencing pufM amplicon libraries. We observed large differences in expression activity among different APB phylogroups. While the total APB community in the Římov Reservoir was dominated by Betaproteobacteria, Alphaproteobacteria prevailed in the active library. A different situation was encountered in the oligotrophic lake Cep where Betaproteobacteria (order Burkholderiales) dominated both the DNA and RNA libraries. Interestingly, in Cep lake we found smaller amounts of highly active uncultured phototrophic Chloroflexi, as well as phototrophic Gemmatimonadetes. Despite the large diversity of APB communities, light repression of pufM expression seems to be a common feature of all aerobic APB present in the studied lakes.

Microbial community structure associated with submarine groundwater discharge in northern Java (Indonesia)

Submarine groundwater discharge (SGD) can be an important pathway for chemical or biological pollutants from land to the ocean around the world. However, studies on the microbial communities associated with SGD in Southeast Asia, which has been hypothesized as SGD hotspot, remain scarce. In this study, we examined the microbial community composition with 16S rRNA gene sequencing along the hydrological continuum of an SGD site in a tropical urban area of Indonesia. Of the observed parameters in this study, salinity and temperature were the most determinant variables explaining patterns in microbial community composition. The bacterial taxon Burkholderiaceae was predominantly found in low salinity samples, including those from terrestrial groundwater and brackish pore water, while cyanobacteria of the genus Synechococcus sp. CC9902 were indicative of saline SGD and seawater samples. The composition of microbial taxa in each sample pointed to the influence of shallow terrestrial groundwater in the beach pore water, while seawater recirculation dominated the SGD sampling points situated further offshore. We identified taxa containing fecal indicators and potential pathogens at the SGD compartments; however, while a likely explanation, we could not conclude with certainty that SGD was a conduit for these bacteria. Overall, the results from this study show that microbial community analysis can highlight hydrological processes and water quality at the SGD site; thus, they could be useful for environmental policymakers to formulate water management strategies in coastal areas.

Effects of residual ozone on the performance of microorganisms treating petrochemical wastewater

This study investigated the effects of residual ozone on the performance of microorganisms treating petrochemical wastewater using batch experiments with low and high ozone dosages (5.0 mg/L and 50.0 mg/L, respectively). The results indicated that the low residual ozone concentration significantly increased COD removal by 24.21% in the biological process compared to control group with no ozone residual, while the high residual ozone concentration showed the opposite effect. In the reactor with low residual ozone concentration (0.45 mg/L), the amount of loosely bound (LB)-extracellular polymeric substances (EPS) in the activated sludge decreased by 23.23%, while the amount of tightly bound (TB)-EPS increased by 129.16% compared to the none-ozone residual reactor. In addition, the low residual ozone was found to improve the bioactivity of activated sludge by 139.73% in the first 30 min of the biological process. In the reactor with high residual ozone concentration (0.91 mg/L), both LB- and TB-EPS of the activated sludge increased, while bioactivity decreased. This implies that low residual ozone in a bio-reactor can enhance microbial activity by increasing contact between the pollutants and cells by removing LB-EPS covering the outer layer of the sludge. The microorganisms in the sludge samples could be classified into three groups representing those that are susceptible to ozone, tolerant to low dose of residual ozone, and resistant to high dose of residual ozone. The resistant bacteria Gemmatimonadaceae uncultured became predominant, with a relative abundance of 11.37%, under low residual ozone conditions, while it decreased at high ozone concentrations. The results showed that a certain amount of residual ozone could stimulate the activity of microorganisms by altering the EPS fraction and structure of the microbial community, and thus it is important for the removal of refractory organics from wastewater in the ozone-biological process.