Identification of sulfur-cycle prokaryotes in a low-sulfate lake (Lake Pavin) using aprA and 16S rRNA gene markers

Actinobacteria produce taste and odor in drinking water reservoir: Community composition dynamics, co-occurrence and inactivation models

Taste and odor (T&O) has become a significant concern for drinking water safety. Actinobacteria are believed to produce T&O during the non-algal bloom period; however, this has not been widely investigated. In this study, the seasonal dynamics of the actinobacterial community structure and inactivation of odor-producing actinobacteria were explored. The results indicated that the diversity and community composition of actinobacteria exhibited significant spatiotemporal distribution. Network analysis and structural equation modeling showed that the actinobacterial community occupied a similar environmental niche, and the major environmental attributes exhibited spatiotemporal dynamics, which affected the actinobacterial community. Furthermore, the two genera of odorous actinobacteria were inactivated in drinking water sources using chlorine. Amycolatopsis spp. have a stronger chlorine resistance ability than Streptomyces spp., indicating that chlorine inactivates actinobacteria by first destroying cell membranes and causing the release of intracellular compounds. Finally, we integrated the observed variability in the inactivation rate of actinobacteria into an expanded Chick-Watson model to estimate its effect on inactivation. These findings will deepen our understanding of the seasonal dynamics of actinobacterial community structure in drinking water reservoirs and provide a foundation for reservoir water quality management strategies.

Mobilization pilot test of PCE sources in the transition zone to aquitards by combining mZVI and biostimulation with lactic acid

The potential toxic and carcinogenic effects of chlorinated solvents in groundwater on human health and aquatic ecosystems require very effective remediation strategies of contaminated groundwater to achieve the low legal cleanup targets required. The transition zones between aquifers and bottom aquitards occur mainly in prograding alluvial fan geological contexts. Hence, they are very frequent from a hydrogeological point of view. The transition zone consists of numerous thin layers of fine to coarse-grained clastic fragments (e.g., medium sands and gravels), which alternate with fine-grained materials (clays and silts). When the transition zones are affected by DNAPL spills, free-phase pools accumulate on the less conductive layers. Owing to the low overall conductivity of this zone, the pools are very recalcitrant. Little field research has been done on transition zone remediation techniques. Injection of iron microparticles has the disadvantage of the limited accessibility of this reagent to reach the entire source of contamination. Biostimulation of indigenous microorganisms in the medium has the disadvantage that few of the microorganisms are capable of complete biodegradation to total mineralization of the parent contaminant and metabolites. A field pilot test was conducted at a site where a transition zone existed in which DNAPL pools of PCE had accumulated. In particular, the interface with the bottom aquitard was where PCE concentrations were the highest. In this pilot test, a combined strategy using ZVI in microparticles and biostimulation with lactate in the form of lactic acid was conducted. Throughout the test it was found that the interdependence of the coupled biotic and abiotic processes generated synergies between these processes. This resulted in a greater degradation of the PCE and its transformation products. With the combination of the two techniques, the mobilization of the contaminant source of PCE was extremely effective.

Evidence of microbial activity in a uranium roll-front deposit: Unlocking their potential role as bioenhancers of the ore genesis

Uranium (U) roll-front deposits constitute a valuable source for an economical extraction by in situ recovery (ISR) mining. Such technology may induce changes in the subsurface microbiota, raising questions about the way their activities could build a functional ecosystem in such extreme environments (i.e.: oligotrophy and high SO₄ concentration and salinity). Additionally, more information is needed to dissipate the doubts about the microbial role in the genesis of such U orebodies. A U roll-front deposit hosted in an aquifer driven system (in Zoovch Ovoo, Mongolia), intended for mining by acid ISR, was previously explored and showed to be governed by a complex bacterial diversity, linked to the redox zonation and the geochemical conditions. Here for the first time, transcriptional activities of microorganisms living in such U ore deposits are determined and their metabolic capabilities allocated in the three redox-inherited compartments, naturally defined by the roll-front system. Several genes encoding for crucial metabolic pathways demonstrated a strong biological role controlling the subsurface cycling of many elements including nitrate, sulfate, metals and radionuclides (e.g.: uranium), through oxidation-reduction reactions. Interestingly, the discovered transcriptional behaviour gives important insights into the good microbial adaptation to the geochemical conditions and their active contribution to the stabilization of the U ore deposits. Overall, evidences on the importance of these microbial metabolic activities in the aquifer system are discussed that may clarify the doubts on the microbial role in the genesis of low-temperature U roll-front deposits, along the Zoovch Ovoo mine.

Aquirufa lenticrescens sp. nov. and Aquirufa aurantiipilula sp. nov.: two new species of a lineage of widespread freshwater bacteria

Two bacterial strains, 9H-EGSE^T and 15D-MOB^T, were isolated from small freshwater habitats located near Salzburg, Austria. They showed the highest 16S rRNA sequence similarities of 100% and 99.9%, respectively, with type strains of species of the genus Aquirufa (Bacteroidota). Genome-based phylogenetic reconstructions with 119 amino acid sequences assigned the new taxa to the two distinct branches of the genus Aquirufa. Whole-genome average nucleotide identities were calculated with all possible pairs belonging to the genus. Values between 75.4% and 88.6% revealed that the two new strains represent each a new species. Like all, so far described members of the genus, they grew aerobically and chemoorganotrophically, were rod-shaped, red-pigmented, and motile by gliding, and showed genome sizes of about 3 Mbp and G + C values of about 40%. They could be distinguished by some phenotypic and chemotaxonomic features from their nearest related species. Until now, strain 9H-EGSE^T is the only one among the Aquirufa strains which contained traces of MK8 as respiratory quinone, and strain 15D-MOB^T is the only one that formed tiny orange globules in liquid medium. The genome of strain 9H-EGSE^T comprised genes for the complete light-harvesting rhodopsin / retinal system, in the case of 15D-MOB^T genes predicted for a nitrous oxide reductase were present. For the two new species of the genus Aquirufa, we propose to establish the names Aquirufa lenticrescens for strain 9H-EGSE^T (= JCM 34077 ^T = CIP 111926 ^T) and Aquirufa aurantiipilula for strain 15D-MOB^T (= JCM 34078 ^T = CIP 111925 ^T).

Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese

Toxic cyanobacterial blooms represent a natural phenomenon caused by a mass proliferation of photosynthetic prokaryotic microorganisms in water environments. Bloom events have been increasingly reported worldwide and their occurrence can pose serious threats to aquatic organisms and human health. In this study, we assessed the microbial composition, with a focus on Cyanobacteria, in Lake Varese, a eutrophic lake located in northern Italy. Water samples were collected and used for obtaining a 16S-based taxonomic profile and performing a shotgun sequencing analysis. The phyla found to exhibit the greatest relative abundance in the lake included Proteobacteria, Cyanobacteria, Actinobacteriota and Bacteroidota. In the epilimnion and at 2.5 × Secchi depth, Cyanobacteria were found to be more abundant compared to the low levels detected at greater depths. The blooms appear to be dominated mainly by the species Lyngbya robusta, and a specific functional profile was identified, suggesting that distinct metabolic processes characterized the bacterial population along the water column. Finally, analysis of the shotgun data also indicated the presence of a large and diverse phage population.

Spatial and temporal dynamics of actinobacteria in drinking water reservoirs: Novel insights into abundance, community structure, and co-existence model

The control of taste and odor (T&O) in drinking water reservoirs is the main challenge for water supply. T&O is mainly derived from actinobacteria during non-algal blooms. However, few studies have investigated the actinobacterial community in reservoirs, especially the effects of water quality parameters on actinobacteria. This study analyzed the environmental driving force of the actinobacterial community composition and change in time and space through structural equations and network in drinking water reservoirs. The results showed a high abundance of actinobacteria, up to 2.7 × 10⁴ actinobacteria per 1 L, in the hypolimnion of the Lijiahe reservoir in September, which is one order of magnitude greater than that in the Jinpen reservoir. The two drinking water reservoirs had similar dominant genera, mainly Sporichthya sp., and Mycobacterium sp., and difference in the actinobacterial proportions. However, there was a large difference at the dominant species. Rhodococcus fascians (4.02%) was the dominant species in the Lijiahe reservoir, while Mycobacterium chlorophenolicum (6.64%) was the dominant species in the Jinpen reservoir. Network analysis revealed that the structure of the network in the Lijiahe reservoir was more unstable; thus, it was vulnerable to environmental disturbances. In addition, a low abundance of species may play a critical role in the actinobacterial community structure of aquatic ecosystems. Structural equation modeling analysis suggested that water temperature, dissolved oxygen, and nutrition were the dominant factors affecting the abundance and community of actinobacteria. Overall, these findings broaden the understanding of the distribution and co-existence of actinobacterial communities in drinking water reservoirs and provide valuable clues for the biological controls of T&O and reservoir management.

Succession of sulfur bacteria during decomposition of cyanobacterial bloom biomass in the shallow Lake Nanhu: An ex situ mesocosm study

Previous studies of the dynamics of sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) have focused on deep stratified lakes. The objective of this study is to present an in-depth investigation of the structure and dynamics of sulfur bacteria (including SRB and SOB) in the water column of shallow freshwater lakes. A cyanobacterial bloom biomass (CBB)-amended mesocosm experiment was conducted in this study, in which water was taken from a shallow eutrophic lake with sulfate levels near 40 mg L^-1. Illumina sequencing was used to investigate SRB and SOB species involved in CBB decomposition and the effects of the increases in sulfate input on the water column microbial community structure. The accumulation of dissolved sulfide (∑H₂S) produced by SRB during CBB decomposition stimulated the growth of SOB, and ∑H₂S was then oxidized back to sulfate by SOB in the water column. Chlorobaculum sequences (the main SOB species in the study) were significantly influenced by increases in sulfate input, with relative abundance increasing approximately four-fold in treatments amended with 40 mg L^-1 sulfate (referred to as 40S) when compared to the treatment without additional sulfate addition (referred to as CU). Additionally, an increase in SOB number was observed from day 26-37, concurrent with the decrease in SRB number, indicating the succession of sulfur bacteria. These findings suggest that biological sulfur oxidation and succession of sulfur bacteria occur in the water column during CBB decomposition in shallow freshwater ecosystems, and the increases in sulfate input stimulate microbial sulfur oxidation.

New insights into the pelagic microorganisms involved in the methane cycle in the meromictic Lake Pavin through metagenomics

Advances in metagenomics have given rise to the possibility of obtaining genome sequences from uncultured microorganisms, even for those poorly represented in the microbial community, thereby providing an important means to study their ecology and evolution. In this study, metagenomic sequencing was carried out at four sampling depths having different oxygen concentrations or environmental conditions in the water column of Lake Pavin. By analyzing the sequenced reads and matching the contigs to the proxy genomes of the closest cultivated relatives, we evaluated the metabolic potential of the dominant planktonic species involved in the methane cycle. We demonstrated that methane-producing communities were dominated by the genus Methanoregula while methane-consuming communities were dominated by the genus Methylobacter, thus confirming prior observations. Our work allowed the reconstruction of a draft of their core metabolic pathways. Hydrogenotrophs, the genes required for acetate activation in the methanogen genome, were also detected. Regarding methanotrophy, Methylobacter was present in the same areas as the non-methanotrophic, methylotrophic Methylotenera, which could suggest a relationship between these two groups. Furthermore, the presence of a large gene inventory for nitrogen metabolism (nitrate transport, denitrification, nitrite assimilation and nitrogen fixation, for instance) was detected in the Methylobacter genome.

Interactions of sulfur and methane-oxidizing bacteria in tropical estuarine sediments

The bacterial oxidation of sulfur and methane is central to the biogeochemical processes in sediments such as the tropical mangrove sediments. However, there is a lacuna of information on the seasonal interactions including the influence of monsoons which is a major driver of seasonal change, on sulfur-oxidizing bacteria (SOB) and methane-oxidizing bacteria (MOB), their activity and the environmental variables. To understand these interactions, the analysis was carried out on sediment samples that were sampled monthly for a year from Chorao mangrove, Goa, southwest coast of India. SOB (3.8×10⁵CFU g^-1) and MOB (0.90×10⁵CFU g^-1) had maximum average abundance in the surface sediments in the post-monsoon and monsoon season, respectively. The mean sulfur-oxidation activity (SOA) of 2.63 mM day^-1 and methane-oxidation activity (MOA) of 110.94 mM day^-1 were highest in surface sediments during the post-monsoon season. Generally, the activity of SOB and MOB in surface sediments of post-monsoon was 2.2 times(×) and 2.8× respectively higher than that in the monsoon season. Among the environmental parameters analyzed, protein and sulfide concentrations significantly (p < 0.001) influenced SOA and MOA, respectively. There was a significant difference in SOA (p < 0.003) and MOA (p < 0.036) in surface sediments between the monsoon and the post-monsoon season. During the monsoon season, when the system is a sink of terrestrial/anthropogenic material, the interrelationship of SOB with MOA (r = 0.617, p < 0.001) and SOB with SOA (r = 0.489, p < 0.05) aids in maintaining the homeostasis of the system.

Spatio-temporal dynamics of sulfur bacteria during oxic--anoxic regime shifts in a seasonally stratified lake

Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria drive major transformations in the sulfur cycle, and play vital roles in oxic--anoxic transitions in lakes and coastal waters. However, information on the succession of these sulfur bacteria in seasonally stratified lakes using molecular biological techniques is scarce. Here, we used 16S rRNA gene amplicon sequencing to study the spatio-temporal dynamics of sulfur bacteria during oxic--anoxic regime shifts in Lake Vechten. Oxygen and sulfate were mixed throughout the water column in winter and early spring. Meanwhile, SRB, green sulfur bacteria (GSB), purple sulfur bacteria (PSB), and colorless sulfur bacteria (CSB) exclusively inhabited the sediment. After the water column stratified, oxygen and nitrate concentrations decreased in the hypolimnion and various SRB species expanded into the anoxic hypolimnion. Consequently, sulfate was reduced to sulfide, stimulating the growth of PSB and GSB in the metalimnion and hypolimnion during summer stratification. When hypoxia spread throughout the water column during fall turnover, SRB and GSB vanished from the water column, whereas CSB (mainly Arcobacter) and PSB (Lamprocystis) became dominant and oxidized the accumulated sulfide under micro-aerobic conditions. Our results support the view that, once ecosystems have become anoxic and sulfidic, a large oxygen influx is needed to overcome the anaerobic sulfur cycle and bring the ecosystems back into their oxic state.

Microbial diversity involved in iron and cryptic sulfur cycling in the ferruginous, low-sulfate waters of Lake Pavin

Both iron- and sulfur- reducing bacteria strongly impact the mineralogy of iron, but their activity has long been thought to be spatially and temporally segregated based on the higher thermodynamic yields of iron over sulfate reduction. However, recent evidence suggests that sulfur cycling can predominate even under ferruginous conditions. In this study, we investigated the potential for bacterial iron and sulfur metabolisms in the iron-rich (1.2 mM dissolved Fe2+), sulfate-poor (< 20 μM) Lake Pavin which is expected to host large populations of iron-reducing and iron-oxidizing microorganisms influencing the mineralogy of iron precipitates in its permanently anoxic bottom waters and sediments. 16S rRNA gene amplicon libraries from at and below the oxycline revealed that highly diverse populations of sulfur/sulfate-reducing (SRB) and sulfur/sulfide-oxidizing bacteria represented up to 10% and 5% of the total recovered sequences in situ, respectively, which together was roughly equivalent to the fraction of putative iron cycling bacteria. In enrichment cultures amended with key iron phases identified in situ (ferric iron phosphate, ferrihydrite) or with soluble iron (Fe2+), SRB were the most competitive microorganisms, both in the presence and absence of added sulfate. The large fraction of Sulfurospirillum, which are known to reduce thiosulfate and sulfur but not sulfate, present in all cultures was likely supported by Fe(III)-driven sulfide oxidation. These results support the hypothesis that an active cryptic sulfur cycle interacts with iron cycling in the lake. Analyses of mineral phases showed that ferric phosphate in cultures dominated by SRB was transformed to vivianite with concomitant precipitation of iron sulfides. As colloidal FeS and vivianite have been reported in the monimolimnion, we suggest that SRB along with iron-reducing bacteria strongly influence iron mineralogy in the water column and sediments of Lake Pavin.

Dominance of Sulfuritalea species in nitrate-depleted water of a stratified freshwater lake and arsenate respiration ability within the genus

Facultative autotrophs of the genus Sulfuritalea within the class Betaproteobacteria have been predicted to be an important bacterial population in stratified freshwater lakes based on previous PCR-based studies. Here, we designed a new probe specific for the genus Sulfuritalea and performed catalysed reporter deposition-fluorescence in situ hybridisation to enumerate cells of Sulfuritalea species throughout the water column in a stratified freshwater lake. The cells stained with the Sulfuritalea-specific probe were detected in all hypoxic water samples collected in different seasons and years. Their abundance ranged from 1.4 × 10⁴ to 2.1 × 10⁵ cells ml^-1 , corresponding to 0.5-5.5% of the total DAPI-stained cells and 2.3-15% of the total bacterial cells. A high abundance of Sulfuritalea species was recorded in hypoxic water samples without nitrate, which is the only known anaerobic electron acceptor for Sulfuritalea. Nitrate-independent anaerobic respiration was further investigated using a single cultured representative of this genus, and its growth via arsenate respiration was experimentally demonstrated. In conclusion, Sulfuritalea species were found to be a major component of the planktonic bacterial community in nitrate-depleted hypoxic water, where arsenate respiration is one of the possible energy metabolisms of Sulfuritalea.

Nutrient Acquisition and the Metabolic Potential of Photoferrotrophic Chlorobi

Anoxygenic photosynthesis evolved prior to oxygenic photosynthesis and harnessed energy from sunlight to support biomass production on the early Earth. Models that consider the availability of electron donors predict that anoxygenic photosynthesis using Fe(II), known as photoferrotrophy, would have supported most global primary production before the proliferation of oxygenic phototrophs at approximately 2.3 billion years ago. These photoferrotrophs have also been implicated in the deposition of banded iron formations, the world's largest sedimentary iron ore deposits that formed mostly in late Archean and early Proterozoic Eons. In this work we present new data and analyses that illuminate the metabolic capacity of photoferrotrophy in the phylum Chlorobi. Our laboratory growth experiments and biochemical analyses demonstrate that photoferrotrophic Chlorobi are capable of assimilatory sulfate reduction and nitrogen fixation under sulfate and nitrogen limiting conditions, respectively. Furthermore, the evolutionary histories of key enzymes in both sulfur (CysH and CysD) and nitrogen fixation (NifDKH) pathways are convoluted; protein phylogenies, however, suggest that early Chlorobi could have had the capacity to assimilate sulfur and fix nitrogen. We argue, then, that the capacity for photoferrotrophic Chlorobi to acquire these key nutrients enabled them to support primary production and underpin global biogeochemical cycles in the Precambrian.

Ecosystem activation system (EAS) technology for remediation of eutrophic freshwater

Ecosystem activation system (EAS) was developed to create beneficial conditions for microbiome recovery and then restore and maintain the ecological integrity (microbial community, phytoplankton, zooplankton) for eutrophic freshwater rehabilitation. A 30 day’s filed test of EAS indicated that over 50% of contaminant was removed and the algae visibly disappeared. EAS treatment 2.5-fold increased the diversity of microbial community and changed the microbial community structure (e.g., two and three-fold decrease in the amount of Flavobacterium and Pseudomonas, typical abundant species of eutrophic freshwater, respectively). Further, the diversity of phytoplankton and zooplankton of treated water suggested that these species were diverse. Representative phytoplankton of eutrophic freshwater, Chlorella and Chlamydomonas were undetectable. The possible mechanism of EAS is restoring the trophic levels of the water body via bottom-up approach by microbial community.

Diversity and Composition of Sulfate-Reducing Microbial Communities Based on Genomic DNA and RNA Transcription in Production Water of High Temperature and Corrosive Oil Reservoir

Deep subsurface petroleum reservoir ecosystems harbor a high diversity of microorganisms, and microbial influenced corrosion is a major problem for the petroleum industry. Here, we used high-throughput sequencing to explore the microbial communities based on genomic 16S rDNA and metabolically active 16S rRNA analyses of production water samples with different extents of corrosion from a high-temperature oil reservoir. Results showed that Desulfotignum and Roseovarius were the most abundant genera in both genomic and active bacterial communities of all the samples. Both genomic and active archaeal communities were mainly composed of Archaeoglobus and Methanolobus. Within both bacteria and archaea, the active and genomic communities were compositionally distinct from one another across the different oil wells (bacteria p = 0.002; archaea p = 0.01). In addition, the sulfate-reducing microorganisms (SRMs) were specifically assessed by Sanger sequencing of functional genes aprA and dsrA encoding the enzymes adenosine-5'-phosphosulfate reductase and dissimilatory sulfite reductase, respectively. Functional gene analysis indicated that potentially active Archaeoglobus, Desulfotignum, Desulfovibrio, and Thermodesulforhabdus were frequently detected, with Archaeoglobus as the most abundant and active sulfate-reducing group. Canonical correspondence analysis revealed that the SRM communities in petroleum reservoir system were closely related to pH of the production water and sulfate concentration. This study highlights the importance of distinguishing the metabolically active microorganisms from the genomic community and extends our knowledge on the active SRM communities in corrosive petroleum reservoirs.

Millions of Boreal Shield Lakes can be used to Probe Archaean Ocean Biogeochemistry

Life originated in Archaean oceans, almost 4 billion years ago, in the absence of oxygen and the presence of high dissolved iron concentrations. Early Earth oxidation is marked globally by extensive banded iron formations but the contributing processes and timing remain controversial. Very few aquatic habitats have been discovered that match key physico-chemical parameters of the early Archaean Ocean. All previous whole ecosystem Archaean analogue studies have been confined to rare, low sulfur, and permanently stratified lakes. Here we provide first evidence that millions of Boreal Shield lakes with natural anoxia offer the opportunity to constrain biogeochemical and microbiological aspects of early Archaean life. Specifically, we combined novel isotopic signatures and nucleic acid sequence data to examine processes in the anoxic zone of stratified boreal lakes that are naturally low in sulfur and rich in ferrous iron, hallmark characteristics predicted for the Archaean Ocean. Anoxygenic photosynthesis was prominent in total water column biogeochemistry, marked by distinctive patterns in natural abundance isotopes of carbon, nitrogen, and iron. These processes are robust, returning reproducibly after water column re-oxygenation following lake turnover. Evidence of coupled iron oxidation, iron reduction, and methane oxidation affect current paradigms of both early Earth and modern aquatic ecosystems.

Photoferrotrophy: Remains of an Ancient Photosynthesis in Modern Environments

Photoferrotrophy, the process by which inorganic carbon is fixed into organic matter using light as an energy source and reduced iron [Fe(II)] as an electron donor, has been proposed as one of the oldest photoautotrophic metabolisms on Earth. Under the iron-rich (ferruginous) but sulfide poor conditions dominating the Archean ocean, this type of metabolism could have accounted for most of the primary production in the photic zone. Here we review the current knowledge of biogeochemical, microbial and phylogenetic aspects of photoferrotrophy, and evaluate the ecological significance of this process in ancient and modern environments. From the ferruginous conditions that prevailed during most of the Archean, the ancient ocean evolved toward euxinic (anoxic and sulfide rich) conditions and, finally, much after the advent of oxygenic photosynthesis, to a predominantly oxic environment. Under these new conditions photoferrotrophs lost importance as primary producers, and now photoferrotrophy remains as a vestige of a formerly relevant photosynthetic process. Apart from the geological record and other biogeochemical markers, modern environments resembling the redox conditions of these ancient oceans can offer insights into the past significance of photoferrotrophy and help to explain how this metabolism operated as an important source of organic carbon for the early biosphere. Iron-rich meromictic (permanently stratified) lakes can be considered as modern analogs of the ancient Archean ocean, as they present anoxic ferruginous water columns where light can still be available at the chemocline, thus offering suitable niches for photoferrotrophs. A few bacterial strains of purple bacteria as well as of green sulfur bacteria have been shown to possess photoferrotrophic capacities, and hence, could thrive in these modern Archean ocean analogs. Studies addressing the occurrence and the biogeochemical significance of photoferrotrophy in ferruginous environments have been conducted so far in lakes Matano, Pavin, La Cruz, and the Kabuno Bay of Lake Kivu. To date, only in the latter two lakes a biogeochemical role of photoferrotrophs has been confirmed. In this review we critically summarize the current knowledge on iron-driven photosynthesis, as a remains of ancient Earth biogeochemistry.

Identity of major sulfur-cycle prokaryotes in freshwater lake ecosystems revealed by a comprehensive phylogenetic study of the dissimilatory adenylylsulfate reductase

Adenylylsulfate reductase is a heterodimeric complex of two subunits, AprB and AprA, and is a key enzyme in dissimilatory sulfate reduction and sulfur oxidation. Common use of aprA as a functional marker gene has revealed the diversity of sulfur-cycle prokaryotes in diverse environments. In this study, we established a comprehensive sequence set of apr genes and employed it to reanalyze apr phylogeny, evaluate the coverage of a widely used primer set (AprA-1-FW/AprA-5-RV), and categorize environmental aprA sequences. Phylogenetic tree construction revealed new members of Apr lineage II and several previously unrecognized lateral gene transfer events. Using the established phylogenetic tree, we classified all previously reported aprA sequences amplified from freshwater lakes with the primer pair AprA-1-FW/AprA-5-RV in addition to the aprA sequences newly retrieved from freshwater lakes; the obtained results were complemented by 16S rRNA clone library analysis. Apr-based classifications of some of operational taxonomic units were supported by 16S rRNA-based analysis. This study updates our knowledge on the phylogeny of aprBA and shows the identities of several sulfur-cycle bacteria, which could not be classified to a known taxa until now. The established apr sequence set is publicly available and can be applied to assign environmental sequences to known lineages.

Distribution of Dehalococcoidia in the Anaerobic Deep Water of a Remote Meromictic Crater Lake and Detection of Dehalococcoidia-Derived Reductive Dehalogenase Homologous Genes

Here we describe the natural occurrence of bacteria of the class Dehalococcoidia (DEH) and their diversity at different depths in anoxic waters of a remote meromictic lake (Lake Pavin) using 16S rRNA gene amplicon sequencing and quantitative PCR. Detected DEH are phylogenetically diverse and the majority of 16S rRNA sequences have less than 91% similarity to previously isolated DEH 16S rRNA sequences. To predict the metabolic potential of detected DEH subgroups and to assess if they encode genes to transform halogenated compounds, we enriched DEH-affiliated genomic DNA by using a specific-gene capture method and probes against DEH-derived 16S rRNA genes, reductive dehalogenase genes and known insertion sequences. Two reductive dehalogenase homologous sequences were identified from DEH-enriched genomic DNA, and marker genes in the direct vicinity confirm that gene fragments were derived from DEH. The low sequence similarity with known reductive dehalogenase genes suggests yet-unknown catabolic potential in the anoxic zone of Lake Pavin.

Exploring the diversity of Acinetobacter populations in river water with genus-specific primers and probes

This study aimed to explore the diversity of river water Acinetobacter populations using culture-dependent and -independent methods. Pyrosequencing indicated that 1.5% of the total sequences from Qiandeng River water were classified as Acinetobacter. Twelve Acinetobacter strains were isolated from three different sampling sites of the Qiandeng River. Based on culture-dependent methods, A. johnsonii, A. lwoffii and A. guillouiae were the most abundantly represented Acinetobacter strains among the upper, middle and downstream populations of the river. Probing of three Acinetobacter-enriched 16S rRNA gene libraries with the Acinetobacter specific probe Act660F revealed 42 unique 16S rRNA gene sequences exhibiting a similarity of 94.9-99.9% with the known Acinetobacter strains. Among the uncultured Acinetobacter sequences, 50%, 58.3% and 68.8% of those obtained from upstream sampling site A, middle stream sampling site B and downstream sampling site C were phylogenetically located within Group I. This Group represented the most abundant strains of Acinetobacter populations in river water based on culture-independent methods. The results indicated that culture-independent methods provide more detailed information on the diversity of Acinetobacter populations than that based on culture-dependent methods. Therefore, the development of new and efficient isolation methods to identify uncultured Acinetobacter species is required.

Community structure of planktonic methane-oxidizing bacteria in a subtropical reservoir characterized by dominance of phylotype closely related to nitrite reducer

Methane-oxidizing bacteria (MOB) gain energy from the oxidation of methane and may play important roles in freshwater ecosystems. In this study, the community structure of planktonic MOB was investigated in a subtropical reservoir. Bacterial community structure was investigated through the analysis of the 16S rRNA gene. Three groups of phylogenetically distinct MOB were detected in the clone libraries of polymerase chain reaction products obtained with universal primers. The groups belonged to the class Gammaproteobacteria, the class Alphaproteobacteria, and the candidate phylum NC10. The last group, which consists of close relatives of the nitrite reducer ‘Candidatus Methylomirabilis oxyfera', was frequently detected in the clone libraries of deep-water environments. The presence of 3 groups of MOB in deep water was also shown by a cloning analysis of the pmoA gene encoding particulate methane monooxygenase. The dominance of ‘M. oxyfera'-like organisms in deep water was confirmed by catalyzed reporter deposition–fluorescence in situ hybridization, in which cells stained with a specific probe accounted for 16% of total microbial cells. This is the first study to demonstrate that close relatives of the nitrite reducer can be major component of planktonic MOB community which may affect carbon flow in aquatic ecosystems.

Analysis of the microbial community in moderately acidic drainage from the Yanahara pyrite mine in Japan

Acid rock drainage (ARD) originating from the Yasumi-ishi tunnel near the main tunnel of the Yanahara mine in Japan was characterized to be moderately acidic (pH 4.1) and contained iron at a low concentration (51 mg/L). The composition of the microbial community was determined by sequence analysis of 16S rRNA genes using PCR and denaturing gradient gel electrophoresis. The analysis of the obtained sequences showed their similarity to clones recently detected in other moderately acidic mine drainages. Uncultured bacteria related to Ferrovum- and Gallionella-like clones were dominant in the microbial community. Analyses using specific primers for acidophilic iron- or sulfur-oxidizing bacteria, Acidithiobacillus ferrooxidans, Leptospirillum spp., Acidithiobacillus caldus, Acidithiobacillus thiooxidans, and Sulfobacillus spp. revealed the absence of these bacteria in the microbial community in ARD from the Yasumi-ishi tunnel. Clones affiliated with a member of the order Thermoplasmatales were detected as the dominant archaea in the ARD microbial population.

Complete genomes of freshwater sulfur oxidizers Sulfuricella denitrificans skB26 and Sulfuritalea hydrogenivorans sk43H: genetic insights into the sulfur oxidation pathway of betaproteobacteria

Despite detailed studies of marine sulfur-oxidizing bacteria, our knowledge concerning their counterparts in freshwater lake ecosystems is limited. Genome sequencing of the freshwater sulfur-oxidizing betaproteobacteria Sulfuricella denitrificans skB26 and Sulfuritalea hydrogenivorans sk43H have been completed. Strain skB26 possessed a circular plasmid of 86.6-kbp in addition to its chromosome, and an approximate 18-kbp region of the plasmid was occupied by an arxA-like operon, encoding a new clade of anaerobic arsenite oxidase. Multilocus sequence analysis showed that strain skB26 could not be assigned to any existing order; thus a novel order, Sulfuricellales, is proposed. The genomes of strains skB26 and sk43H were examined, focusing on the composition and the phylogeny of genes involved in the oxidation of inorganic sulfur compounds. Strains skB26 and sk43H shared a common pathway, which consisted of Sqr, SoxEF, SoxXYZAB, Dsr proteins, AprBA, Sat, and SoeABC. Comparative genomics of betaproteobacterial sulfur oxidizers showed that this pathway was also shared by the freshwater sulfur oxidizers Thiobacillus denitrificans and Sideroxydans lithotrophicus. It also revealed the presence of a conserved gene cluster, which was located immediately upstream of the betaproteobacterial dsr operon.

Identification of major planktonic sulfur oxidizers in stratified freshwater lake

Planktonic sulfur oxidizers are important constituents of ecosystems in stratified water bodies, and contribute to sulfide detoxification. In contrast to marine environments, taxonomic identities of major planktonic sulfur oxidizers in freshwater lakes still remain largely unknown. Bacterioplankton community structure was analyzed in a stratified freshwater lake, Lake Mizugaki in Japan. In the clone libraries of 16S rRNA gene, clones very closely related to a sulfur oxidizer isolated from this lake, Sulfuritalea hydrogenivorans, were detected in deep anoxic water, and occupied up to 12.5% in each library of different water depth. Assemblages of planktonic sulfur oxidizers were specifically analyzed by constructing clone libraries of genes involved in sulfur oxidation, aprA, dsrA, soxB and sqr. In the libraries, clones related to betaproteobacteria were detected with high frequencies, including the close relatives of Sulfuritalea hydrogenivorans.

Draft genome sequence of a psychrotolerant sulfur-oxidizing bacterium, Sulfuricella denitrificans skB26, and proteomic insights into cold adaptation

Except for several conspicuous cases, very little is known about sulfur oxidizers living in natural freshwater environments. Sulfuricella denitrificans skB26 is a psychrotolerant sulfur oxidizer recently isolated from a freshwater lake as a representative of a new genus in the class Betaproteobacteria. In this study, an approximately 3.2-Mb draft genome sequence of strain skB26 was obtained. In the draft genome, consisting of 23 contigs, a single rRNA operon, 43 tRNA genes, and 3,133 coding sequences were identified. The identified genes include those required for sulfur oxidation, denitrification, and carbon fixation. Comparative proteomic analysis was conducted to assess cold adaptation mechanisms of this organism. From cells grown at 22°C and 5°C, proteins were extracted for analysis by nano-liquid chromatography-electrospray ionization-tandem mass spectrometry. In the cells cultured at 5°C, relative abundances of ribosomal proteins, cold shock proteins, and DEAD/DEAH box RNA helicases were increased in comparison to those at 22°C. These results suggest that maintenance of proper translation is critical for growth under low-temperature conditions, similar to the case for other cold-adapted prokaryotes.

Identification of microbial communities involved in the methane cycle of a freshwater meromictic lake

Lake Pavin is a meromictic crater lake located in the French Massif Central area. In this ecosystem, most methane (CH(4)) produced in high quantity in the anoxic bottom layers, and especially in sediments, is consumed in the water column, with only a small fraction of annual production reaching the atmosphere. This study assessed the diversity of methanogenic and methanotrophic populations along the water column and in sediments using PCR and reverse transcription-PCR-based approaches targeting functional genes, i.e. pmoA (α-subunit of the particulate methane monooxygenase) for methanotrophy and mcrA (α-subunit of the methyl-coenzyme M reductase) for methanogenesis as well as the phylogenetic 16S rRNA genes. Although methanogenesis rates were much higher in sediments, our results confirm that CH(4) production also occurs in the water column where methanogens were almost exclusively composed of hydrogenotrophic methanogens, whereas both hydrogenotrophs and acetotrophs were almost equivalent in the sediments. Sequence analysis of markers, pmoA and the 16S rRNA gene, suggested that Methylobacter may be an important group actively involved in CH(4) oxidation in the water column. Two main phylotypes were characterized, one of which could consume CH(4) under conditions where the oxygen amount is undetectable.