Terrabacteria: redefining bacterial envelope diversity, biogenesis and evolution

The bacterial envelope is one of the oldest and most essential cellular components and has been traditionally divided into Gram-positive (monoderm) and Gram-negative (diderm). Recent landmark studies have challenged a major paradigm in microbiology by inferring that the last bacterial common ancestor had a diderm envelope and that the outer membrane (OM) was lost repeatedly in evolution to give rise to monoderms. Intriguingly, OM losses appear to have occurred exclusively in the Terrabacteria, one of the two major clades of bacteria. In this Review, we present current knowledge about the Terrabacteria. We describe their diversity and phylogeny and then highlight the vast phenotypic diversity of the Terrabacteria cell envelopes, which display large deviations from the textbook examples of diderms and monoderms, challenging the classical Gram-positive-Gram-negative divide. We highlight the striking differences in the systems involved in OM biogenesis in Terrabacteria with respect to the classical diderm experimental models and how they provide novel insights into the diversity and biogenesis of the bacterial cell envelope. We also discuss the potential evolutionary steps that might have led to the multiple losses of the OM and speculate on how the very first OM might have emerged before the last bacterial common ancestor.

Unveiling the influence of microaeration and sludge recirculation on enhancement of pharmaceutical removal and microbial community change of the novel anaerobic baffled biofilm - membrane bioreactor in treating building wastewater

This research aims to conduct a comparative investigation of the role played by microaeration and sludge recirculation in the novel anaerobic baffled biofilm-membrane bioreactor (AnBB-MBR) for enhancing pharmaceutical removal from building wastewater. Three AnBB-MBRs - R1: AnBB-MBR, R2: AnBB-MBR with microaeration and R3: AnBB-MBR with microaeration and sludge recirculation - were operated simultaneously to remove Ciprofloxacin (CIP), Caffeine (CAF), Sulfamethoxazole (SMX) and Diclofenac (DCF) from real building wastewater at the hydraulic retention time (HRT) of 30 h for 115 days. From the removal profiles of the targeted pharmaceuticals in the AnBB-MBRs, it was found that the fixed-film compartment (C1) could significantly reduce the targeted pharmaceuticals. The remaining pharmaceuticals were further removed with the microaeration compartment. R2 exhibited the utmost removal efficiency for CIP (78.0 %) and DCF (40.8 %), while SMX was removed most successfully by R3 (microaeration with sludge recirculation) at 91.3 %, followed by microaeration in R2 (88.5 %). For CAF, it was easily removed by all AnBB-MBR systems (>90 %). The removal mechanisms indicate that the microaeration in R2 facilitated the adsorption of CIP onto microaerobic biomass, while the enhanced biodegradation of CAF, SMX and DCF was confirmed by batch biotransformation kinetics and the adsorption isotherms of the targeted pharmaceuticals. The microbial groups involved in biodegradation of the targeted compounds under microaeration were identified as nitrogen removal microbials (Nitrosomonas, Nitrospira, Thiobacillus, and Denitratisoma) and methanotrophs (Methylosarcina, Methylocaldum, and Methylocystis). Overall, explication of the integration of AnBB-MBR with microaeration (R2) confirmed it as a prospective technology for pharmaceutical removal from building wastewater due to its energy-efficient approach characterized by minimal aeration supply.

Comparison of anaerobic digestion of starch- and petro-based bioplastic under hydrogen-rich conditions

To identify an economically viable waste management system for bioplastics, thermoplastic starch (TPS) and poly(butylene adipate-co-terephthalate) (PBAT) were anaerobically digested under hydrogen (H2)/carbon dioxide (CO2) and nitrogen (N2) gas-purged conditions to compare methane (CH4) production and biodegradation. Regardless of the type of bioplastics, CH4 production was consistently higher with H2/CO2 than with N2. The highest amount of CH4 was produced at 307.74 mL CH4/g volatile solids when TPS digested with H2/CO2. A stepwise increased in CH4 yield was observed, with a nominal initial increment followed by accelerated methanogenesis conversion as H2 was depleted. This may be attributed to a substantial shift in the microbial structure from hydrogenotrophic methanogen (Methanobacteriales and Methanomicrobiales) to heterotrophs (Spirochaetia). In contrast, no significant change was observed with PBAT, regardless of the type of purged gas. TPS was broken down into numerous derivatives, including volatile fatty acids. TPS produced more byproducts with H2/CO2 (i.e., 430) than with N2 (i.e., 320). In contrast, differential scanning calorimetry analysis on PBAT revealed an increase in crystallinity from 10.20 % to 12.31 % and 11.36 % in the H2/CO2- and N2-purged conditions, respectively, after 65 days of testing. PBAT surface modifications were characterized via Fourier transform infrared spectroscopy and scanning electron microscopy. The results suggest that the addition of H2/CO2 can enhance the CH4 yield and increase the breakdown rate of TPS more than that of PBAT. This study provides novel insights into the CH4 production potential of two bioplastics with different biodegradabilities in H2/CO2-mediated anaerobic digestion systems.

Judicial Opinion 129

Opinion 129 addresses the status of Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980). The name has the category 'division' and was included in the Approved Lists of Bacterial Names, although that category had previously been removed from the International Code of Nomenclature of Bacteria (1975 revision onwards). When the category 'phylum' was introduced into the International Code of Nomenclature of Prokaryotes (ICNP) in 2021, equivalence between 'phylum' and 'division' was not stipulated. Since the definition of the taxonomic categories and their relative order is one of the principal tasks of every code of nomenclature, the inclusion of Firmicutes corrig. Gibbons and Murray 1978 in the Approved Lists was an error. The name is either not validly published or illegitimate because its category is not covered by the ICNP. If Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980) was a validly published phylum name, it would be illegitimate because it would contravene Rule 8, which does not permit any deviation from the requirement to derive a phylum name from the name of the type genus. Since Firmicutes corrig. Gibbons and Murray 1978 is also part of a 'misfitting megaclassification' recognized in Opinion 128, the name is rejected, without any pre-emption regarding a hypothetically validly published name Firmicutes at the rank of phylum. Gracilicutes Gibbons and Murray 1978 (Approved Lists 1980) and Anoxyphotobacteriae Gibbons and Murray 1978 (Approved Lists 1980) are also rejected. The validly published phylum names have a variety of advantages over their not validly published counterparts and cannot be replaced with ad hoc names suggested in the literature. To ease the transition, it is recommended to mention the not validly published phylum names which strongly deviate in spelling from their validly published counterparts along with the latter in publications during the next years.

Effects of microaeration and sludge recirculation on VFA and nitrogen removal, membrane fouling reduction and microbial community of the anaerobic baffled biofilm-membrane bioreactor in treating building wastewater

A novel anaerobic baffled biofilm-membrane bioreactor (AnBB-MBR) with microaeration of 0.62 LO2/LFeed was developed to improve VFA and nitrogen removal from building wastewater. Three different membrane bioreactor systems - R1: AnBB-MBR (without microaeration); R2: AnBB-MBR with microaeration; and R3: AnBB-MBR with integrated microaeration and sludge recirculation - were operated in parallel at the same hydraulic retention time of 20 h and sludge retention time of 100 d. The microaeration promoted greater microbial richness and diversity, which could significantly enhance the removal of acetic acid and dissolved methane in the R2 and R3 systems. Moreover, the partial nitrification and the ability of anammox (Candidatus Brocadia) to thrive in R2 enabled NH4+-N removal to be enhanced by up to 57.8 %. The worst membrane fouling was found in R1 due to high amount of protein as well as fine particles (0.5-5.0 μm) acting as foulants that contributed to pore blocking. While the integration of sludge recirculation with microaeration in R3 was able to improve the membrane permeate flux slightly as compared to R2. Therefore, the AnBB-MBR integrated with a microaeration system (R2) can be considered as promising technology for building wastewater treatment when considering VFA and nutrient removal and an energy-saving approach with low aeration intensity.

Microbiological characterization of biofilm from different immobilization structures used in submersed aerobic biofilters in domestic effluent treatment at the city of Joinville, Brazil

The objective of this work was to develop a polymeric structure for a biofiltration unit of domestic effluents through microbiological immobilization, capable of promoting the efficient removal of pollutants, meeting local/national Brazilian standards and/or legislation while providing low environmental impact on their production. Four different structures were tested, namely, polypropylene casings without filling material (TF1); polypropylene casings filled with expanded polystyrene grains (TF2); polypropylene casings, filled with polyurethane foam (TF3); and polypropylene casings, filled with polyvinyl chloride pellets (TF4). A flow of 0.216 m3 d-1 was applied to the system, and the biofilters operated in sequential batches with a hydraulic retention time of 6 h. The efficiency potential of the four immobilization structures was verified regarding biochemical and chemical oxygen demand, total ammoniacal nitrogen and total phosphorus. Microbiological analysis of the formed biofilm, performed with the 16S library sequencing method, with amplification of the 16S rRNA V3 and V3-V4 genomic regions, showed a high diversity of microbiological colonization in the four immobilization structures, with better results and consequently greater community stability in TF2. It is recommended using the filter bed made up of unfilled casings, followed by the one filled with expanded polystyrene grains.

Potential for the anaerobic oxidation of benzene and naphthalene in thermophilic microorganisms from the Guaymas Basin

Unsubstituted aromatic hydrocarbons (UAHs) are recalcitrant molecules abundant in crude oil, which is accumulated in subsurface reservoirs and occasionally enters the marine environment through natural seepage or human-caused spillage. The challenging anaerobic degradation of UAHs by microorganisms, in particular under thermophilic conditions, is poorly understood. Here, we established benzene- and naphthalene-degrading cultures under sulfate-reducing conditions at 50°C and 70°C from Guaymas Basin sediments. We investigated the microorganisms in the enrichment cultures and their potential for UAH oxidation through short-read metagenome sequencing and analysis. Dependent on the combination of UAH and temperature, different microorganisms became enriched. A Thermoplasmatota archaeon was abundant in the benzene-degrading culture at 50°C, but catabolic pathways remained elusive, because the archaeon lacked most known genes for benzene degradation. Two novel species of Desulfatiglandales bacteria were strongly enriched in the benzene-degrading culture at 70°C and in the naphthalene-degrading culture at 50°C. Both bacteria encode almost complete pathways for UAH degradation and for downstream degradation. They likely activate benzene via methylation, and naphthalene via direct carboxylation, respectively. The two species constitute the first thermophilic UAH degraders of the Desulfatiglandales. In the naphthalene-degrading culture incubated at 70°C, a Dehalococcoidia bacterium became enriched, which encoded a partial pathway for UAH degradation. Comparison of enriched bacteria with related genomes from environmental samples indicated that pathways for benzene degradation are widely distributed, while thermophily and capacity for naphthalene activation are rare. Our study highlights the capacities of uncultured thermophilic microbes for UAH degradation in petroleum reservoirs and in contaminated environments.

Identification of a deep-branching thermophilic clade sheds light on early bacterial evolution

It has been proposed that early bacteria, or even the last universal common ancestor of all cells, were thermophilic. However, research on the origin and evolution of thermophily is hampered by the difficulties associated with the isolation of deep-branching thermophilic microorganisms in pure culture. Here, we isolate a deep-branching thermophilic bacterium from a deep-sea hydrothermal vent, using a two-step cultivation strategy ("Subtraction-Suboptimal", StS) designed to isolate rare organisms. The bacterium, which we name Zhurongbacter thermophilus 3DAC, is a sulfur-reducing heterotroph that is phylogenetically related to Coprothermobacterota and other thermophilic bacterial groups, forming a clade that seems to represent a major, early-diverging bacterial lineage. The ancestor of this clade might be a thermophilic, strictly anaerobic, motile, hydrogen-dependent, and mixotrophic bacterium. Thus, our study provides insights into the early evolution of thermophilic bacteria.

Phylogenetic Revisit to a Review on Predatory Bacteria

Predatory bacteria, along with the biology of their predatory behavior, have attracted interest in terms of their ecological significance and industrial applications, a trend that has been even more pronounced since the comprehensive review in 2016. This mini-review does not cover research trends, such as the role of outer membrane vesicles in myxobacterial predation, but provides an overview of the classification and newly described taxa of predatory bacteria since 2016, particularly with regard to phylogenetic aspects. Among them, it is noteworthy that in 2020 there was a major phylogenetic reorganization that the taxa hosting Bdellovibrio and Myxococcus, formerly classified as Deltaproteobacteria, were proposed as the new phyla Bdellovibrionota and Myxococcota, respectively. Predatory bacteria have been reported from other phyla, especially from the candidate divisions. Predatory bacteria that prey on cyanobacteria and predatory cyanobacteria that prey on Chlorella have also been found. These are also covered in this mini-review, and trans-phylum phylogenetic trees are presented.

Metagenomic analyses of a microbial assemblage in a subglacial lake beneath the Vatnajökull ice cap, Iceland

Skaftárkatlar are two subglacial lakes located beneath the Vatnajökull ice cap in Iceland associated with geothermal and volcanic activity. Previous studies of these lakes with ribosomal gene (16S rDNA) tag sequencing revealed a limited diversity of bacteria adapted to cold, dark, and nutrient-poor waters. In this study, we present analyses of metagenomes from the lake which give new insights into its microbial ecology. Analyses of the 16S rDNA genes in the metagenomes confirmed the existence of a low-diversity core microbial assemblage in the lake and insights into the potential metabolisms of the dominant members. Seven taxonomic genera, Sulfuricurvum, Sulfurospirillum, Acetobacterium, Pelobacter/Geobacter, Saccharibacteria, Caldisericum, and an unclassified member of Prolixibacteraceae, comprised more than 98% of the rDNA reads in the library. Functional characterisation of the lake metagenomes revealed complete metabolic pathways for sulphur cycling, nitrogen metabolism, carbon fixation via the reverse Krebs cycle, and acetogenesis. These results show that chemolithoautotrophy constitutes the main metabolism in this subglacial ecosystem. This assemblage and its metabolisms are not reflected in enrichment cultures, demonstrating the importance of in situ investigations of this environment.

Cable bacteria accelerate the anaerobic removal of pyrene in black odorous river sediments

Cable bacteria play an essential role in biogeochemical processes in sediments by long-distance electron transport (LDET). A potential relationship has been found between cable bacteria and organic contaminant removal; however, the mechanisms remain unclear. In this study, the response of cable bacteria to pyrene was investigated in sediments with and without pyrene, and the effect of cable bacteria on pyrene removal was explored by connecting and blocking the paths of cable bacteria to the suboxic zones. The results showed that pyrene significantly influenced the microbial community structure and the composition of cable bacteria. The pyrene removal efficiencies significantly increased with the enrichment of cable bacteria, while sulfur-reducing microorganisms and aromatic compound degraders were also significantly enriched and correlated with cable bacteria abundance. Metagenomic analysis showed that cable bacteria have a potential LDET-bound acetate/formate respiratory pathway to gain energy. The presence of pyrene probably selects and enriches cable bacteria with a high tolerance to organic contaminants and changes the related functional microbial community, leading to the acceleration of pyrene removal. This study provides new insights into the interaction mechanisms between contaminants and cable bacteria, shedding light on the applications of cable bacteria in the bioremediation of contaminants in sediments.

Seasonal characterization of the prokaryotic microbiota of full-scale anaerobic UASB reactors treating domestic sewage in southern Brazil

Upflow Anaerobic Sludge Blanket (UASB) reactors are alternatives in the anaerobic treatment of sanitary sewage in different parts of the world; however, in temperate environments, they are subject to strong seasonal influence. Understanding the dynamics of the microbial community in these systems is essential to propose operational alternatives, improve projects and increase the quality of treated effluents. In this study, for one year, high-performance sequencing, associated with bioinformatics tools for taxonomic annotation and functional prediction was used to characterize the microbial community present in the sludge of biodigesters on full-scale, treating domestic sewage at ambient temperature. Among the most representative phyla stood out Desulfobacterota (20.21-28.64%), Proteobacteria (7.48-24.90%), Bacteroidota (10.05-18.37%), Caldisericota (9.49-17.20%), and Halobacterota (3.23-6.55%). By performing a Canonical Correspondence Analysis (CCA), Methanolinea was correlated to the efficiency in removing Chemical Oxygen Demand (COD), Bacteroidetes_VadinHA17 to the production of volatile fatty acids (VFAs), and CI75cm.2.12 at temperature. On the other hand, Desulfovibrio, Spirochaetaceae_uncultured, Methanosaeta, Lentimicrobiaceae_unclassified, and ADurb.Bin063-1 were relevant in shaping the microbial community in a co-occurrence network. Diversity analyses showed greater richness and evenness for the colder seasons, possibly, due to the lesser influence of dominant taxa. Among the principal metabolic functions associated with the community, the metabolism of proteins and amino acids stood out (7.74-8.00%), and the genes related to the synthesis of VFAs presented higher relative abundance for the autumn and winter. Despite the differences in diversity and taxonomic composition, no significant changes were observed in the efficiency of the biodigesters.

Solving the remaining problems with names of classes. Request for an Opinion

The legitimacy, spelling and grammatical gender of names of classes validly published under the International Code of Nomenclature of Prokaryotes (ICNP) is reviewed in the aftermath of the decision to make Rule 8 of the ICNP non-retroactive regarding the formation of such names. This ruling removed most of the nomenclatural uncertainty that affected names of classes but some issues remain to be solved. Some previously legitimate names of classes became illegitimate by this decision while others retained their illegitimacy. The Judicial Commission is asked to conduct according clarifications. It is proposed to place the names at the rank of class Anoxyphotobacteria (Gibbons and Murray 1978) Murray 1988, Archaeobacteria Murray 1988, Bacteria Haeckel 1894 (Approved Lists 1980), Firmibacteria Murray 1988, Microtatobiotes Philip 1956 (Approved Lists 1980), Oxyphotobacteria (ex Gibbons and Murray 1978) Murray 1988, Photobacteria Gibbons and Murray 1978 (Approved Lists 1980), Proteobacteria Stackebrandt et al. 1988, Schizomycetes Nägeli 1857 (Approved Lists 1980) and Scotobacteria Gibbons and Murray 1978 (Approved Lists 1980) on the list of rejected names. It is also requested to orthographically correct the names Aquificae Reysenbach 2002, Chrysiogenetes Garrity and Holt 2002, Gemmatimonadetes Zhang et al. 2003, Opitutae Choo et al. 2007 and Verrucomicrobiae Hedlund et al. 1998.

Insights into ecological roles of uncultivated bacteria in Katase hot spring sediment from long-read metagenomics

Diverse yet-uncultivated bacteria and archaea, i.e., microbial dark matter, are present in terrestrial hot spring environments. Numerous metagenome-assembled genomes (MAGs) of these uncultivated prokaryotes by short-read metagenomics have been reported so far, suggesting their metabolic potential. However, more reliable MAGs, i.e., circularized complete MAGs (cMAGs), have been rarely reported from hot spring environments. Here, we report 61 high-quality (HQ)-MAGs, including 14 cMAGs, of diverse uncultivated bacteria and archaea retrieved from hot spring sediment (52°C, pH 7.2) by highly accurate long-read sequencing using PacBio Sequel II. The HQ MAGs were affiliated with one archaeal and 13 bacterial phyla. Notably, nine of the 14 cMAGs were the first reported cMAGs for the family- to class-level clades that these cMAGs belonged to. The genome information suggests that the bacteria represented by MAGs play a significant role in the biogeochemical cycling of carbon, nitrogen, iron, and sulfur at this site. In particular, the genome analysis of six HQ MAGs including two cMAGs of Armatimonadota, of which members are frequently abundant in hot spring environments, predicts that they are aerobic, moderate thermophilic chemoorganoheterotrophs, and potentially oxidize and/or reduce iron. This prediction is consistent with the environmental conditions where they were detected. Our results expand the knowledge regarding the ecological potential of uncultivated bacteria in moderately-high-temperature environments.

Deciphering the internal mechanisms of ciprofloxacin affected anaerobic digestion, its degradation and detoxification mechanism

Ciprofloxacin (CIP) is widely used in livestock farms, but the internal mechanism of the effect of residual CIP in actual livestock wastewater on anaerobic digestion (AD) performance remains unknown. This study examined the dose-specific effects of CIP (0.5-2 mg/L) on livestock wastewater AD by analyzing acidogenesis and methanogenesis. 0.5 mg/L CIP promoted methane production by facilitating acidogenesis and acetogenesis. Compared with the control, the cumulative methane production increased from 331.38 to 407.44 mL/g VS at a dose of 0.5 mg/L, an increase of 22.95 %. However, as the dose of CIP increased, the cumulative methane production gradually decreased to 217.64 mL/g VS (2 mg/L). Microbial community analysis revealed that CIP had the greatest impact on methane production by influencing the activity of acidogenic bacteria. Meanwhile, acidogenesis was critical for CIP degradation. In acidogenesis, hydroxylation, amination, defluorination, decarboxylation, and piperazine ring breaking not only degraded CIP but also reduced its toxicity. Therefore, a large number of intermediates could be continuously degraded by microorganisms. However, as the dosage of CIP increased, the ability of microorganisms to degrade intermediates decreased.

Lactate as an effective electron donor in the sulfate reduction: impacts on the microbial diversity

The competition between sulfate-reducing bacteria and methane-producing archaea has a major influence on organic matter removal, as well as the success of sulfidogenic systems. This study investigated the performance of six batch sulfidogenic reactors in response to different COD/sulfate ratios (1.0 and 2.0) and electron donors (cheese whey, ethanol, and sodium lactate) by evaluating the biochemical mechanisms of sulfate reduction, organic matter oxidation, and microbial structure modification. A COD/sulfate ratio of 1.0 resulted in high sulfidogenic activity for all electron donors, thereby achieving a nearly 80% sulfate removal. Lactate provided high sulfate removal rates at COD/sulfate ratios of 1.0 (80%) and 2.0 (90%). A COD/sulfate ratio of 2.0 decreased the sulfate removal rates by 25 and 28% when ethanol and cheese whey were used as substrates. The sulfate-reducing bacteria populations increased using ethanol and lactate at a COD/sulfate ratio of 1.0. Particularly, Desulfovibrio, Clostridium, and Syntrophobacter were predominant. Influent composition and COD/sulfate ratio influenced the relative abundance of the microbial communities. Therefore, controlling these parameters may facilitate the wastewater treatment with high sulfate levels through bacterial activity.

Quorum quenching of autoinducer 2 increases methane production in anaerobic digestion of waste activated sludge

The ubiquitous signaling molecule autoinducer 2 (AI-2) is involved in intra- and interspecies communication, most notably between Gram-negative and Gram-positive bacteria. AI-2 accumulates during the exponential phase of the Escherichia coli (E. coli) monoculture and then rapidly decreases upon entry into the stationary phase. However, deleting both the genes encoding AI-2 synthase (LuxS) and the lsr operon regulator (LsrR) in the E. coli genome causes impaired AI-2 production and continuous AI-2 scavenging from the environment. This genetically-engineered E. coli mutant capable of quenching AI-2 quorum sensing (QS) system was utilized to evaluate the effect of AI-2 quenching on the anaerobic digestion of waste activated sludge (WAS) because the role of QS system via AI-2 in the process remains obscure. In this study, E. coli ∆luxS lsrR mutant cells were microencapsulated in sodium alginate beads and incubated with WAS anaerobically. After 15 days of anaerobic fermentation, the WAS containing double mutant cells produced significantly more methane than that of the parent E. coli cells. AI-2 quenching occurred concurrently with a shift of microbial communities that contribute to increasing acetate consumption by the Methanosarcina spp. resulting in an increase in methane production. KEY POINTS: • Impact of autoinducer 2 quenching in complex bacterial populations were determined. • Key microorganisms contributing to the increase of methane in WAS anaerobic digestion were found. • The AI-2 quenching is a potential regulatory in wastewater treatment and bioenergy research.

Spatial Variation and Environmental Parameters Affecting the Abundant and Rare Communities of Bacteria and Archaea in the Sediments of Tropical Urban Reservoirs

Microbial communities in freshwater sediments play an important role in organic matter remineralization, contributing to biogeochemical cycles, nutrient release, and greenhouse gases emissions. Bacterial and archaeal communities might show spatial or seasonal patterns and were shown to be influenced by distinct environmental parameters and anthropogenic activities, including pollution and damming. Here, we determined the spatial variation and the environmental variables influencing the abundant and rare bacterial and archaeal communities in the sediments of eutrophic-hypereutrophic reservoirs from a tropical urban area in Brazil. The most abundant microbes included mainly Anaerolineae and Deltaproteobacteria genera from the Bacteria domain, and Methanomicrobia genera from the Archaea domain. Microbial communities differed spatially in each reservoir, reflecting the establishment of specific environmental conditions. Locations with better or worst water quality, or close to a dam, showed more distinct microbial communities. Besides the water column depth, microbial communities were affected by some pollution indicators, including total phosphorus, orthophosphate, electrical conductivity, and biochemical oxygen demand. Distinct proportions of variation were explained by spatial and environmental parameters for each microbial community. Furthermore, spatial variations in environmental parameters affecting these communities, especially the most distinct ones, contributed to microbial variations mediated by spatial and environmental properties together. Finally, our study showed that different pressures in each reservoir affected the sediment microbiota, promoting different responses and possible adaptations of abundant and rare bacterial and archaeal communities.

Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing

Earth’s mantle releases 38.7 ± 2.9 Tg/yr CO₂ along with other reduced and oxidized gases to the atmosphere shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we perform comparative metagenomics coupled to geochemical measurements of deep subsurface fluids from a cold-water geyser driven by mantle degassing. Key organisms belonging to uncultivated Candidatus Altiarchaeum show a global biogeographic pattern and site-specific adaptations shaped by gene loss and inter-kingdom horizontal gene transfer. Comparison of the geyser community to 16 other publicly available deep subsurface sites demonstrate a conservation of chemolithoautotrophic metabolism across sites. In silico replication measures suggest a linear relationship of bacterial replication with ecosystems depth with the exception of impacted sites, which show near surface characteristics. Our results suggest that subsurface ecosystems affected by geological degassing are hotspots for microbial life in the deep biosphere.

Geological degassing can impact subsurface metabolism. Here, the authors describe microbial communities from a cold-water geyser are described and compared with other deep subsurface sites, finding a key role for an uncultivated archaeon.

Influence of cosubstrate and hydraulic retention time on the removal of drugs and hygiene products in sanitary sewage in an anaerobic Expanded Granular Sludge Bed reactor

Diclofenac (DCF), ibuprofen (IBU), propranolol (PRO), triclosan (TCS) and linear alkylbenzene sulfonate (LAS) can be recalcitrant in Wastewater Treatment Plants (WWTP). The removal of these compounds was investigated in scale-up (69 L) Expanded Granular Sludge Bed (EGSB) reactor, fed with sanitary sewage from the São Carlos-SP (Brazil) WWTP and 200 mg L^-1 of ethanol. The EGSB was operated in three phases: (I) hydraulic retention time (HRT) of 36±4 h; (II) HRT of 20±2 h and (III) HRT of 20±2 h with ethanol. Phases I and II showed no significant difference in the removal of LAS (63 ± 11-65 ± 12 %), DCF (37 ± 18-35 ± 11 %), IBU (43 ± 18-44 ± 16 %) and PRO (46 ± 25-51 ± 23 %) for 13±2-15 ± 2 mg L^-1, 106 ± 32-462 ± 294 μg L^-1, 166 ± 55-462 ± 213 μg L^-1 and 201 ± 113-250 ± 141 μg L^-1 influent, respectively. Higher TCS removal was obtained in phase I (72 ± 17 % for 127 ± 120 μg L^-1 influent) when compared to phase II (51 ± 13 % for 135 ± 119 μg L^-1 influent). This was due to its greater adsorption (40 %) in the initial phase. Phase III had higher removal of DCF (42 ± 10 % for 107 ± 26 μg L^-1 influent), IBU (50 ± 15 % for 164 ± 47 μg L^-1 influent) and TCS (85 ± 15 % for 185 ± 148 μg L^-1 influent) and lower removal of LAS (35 ± 14 % for 12 ± 3 mg L^-1 influent) and PRO (-142 ± 177 % for 188 ± 88 μg L^-1 influent). Bacteria similar to Syntrophobacter, Smithella, Macellibacteroides, Syntrophus, Blvii28_wastewater-sludge_group and Bacteroides were identified in phase I with relative abundance of 3.1 %-4.7 %. Syntrophobacter was more abundant (15.4 %) in phase II, while in phase III, it was Smithella (12.7 %) and Caldisericum (15.1 %). Regarding the Archaea Domain, Methanosaeta was more abundant in phases I (84 %) and II (67 %), while in phase III it was Methanobacterium (86 %).

Valid publication of the names of forty-two phyla of prokaryotes

After the International Committee on Systematics of Prokaryotes (ICSP) had voted to include the rank of phylum in the rules of the International Code of Nomenclature of Prokaryotes (ICNP), and following publication of the decision in the IJSEM, we here present names and formal descriptions of 42 phyla to effect valid publication of their names, based on genera as the nomenclatural types.

Discovery of ancestral L-ornithine and L-lysine decarboxylases reveals parallel, pseudoconvergent evolution of polyamine biosynthesis

Polyamines are fundamental molecules of life, and their deep evolutionary history is reflected in extensive biosynthetic diversification. The polyamines putrescine, agmatine, and cadaverine are produced by pyridoxal 5'-phosphate-dependent L-ornithine, L-arginine, and L-lysine decarboxylases (ODC, ADC, LDC), respectively, from both the alanine racemase (AR) and aspartate aminotransferase (AAT) folds. Two homologous forms of AAT-fold decarboxylase are present in bacteria: an ancestral form and a derived, acid-inducible extended form containing an N-terminal fusion to the receiver-like domain of a bacterial response regulator. Only ADC was known from the ancestral form and limited to the Firmicutes phylum, whereas extended forms of ADC, ODC, and LDC are present in Proteobacteria and Firmicutes. Here, we report the discovery of ancestral form ODC, LDC, and bifunctional O/LDC and extend the phylogenetic diversity of functionally characterized ancestral ADC, ODC, and LDC to include phyla Fusobacteria, Caldiserica, Nitrospirae, and Euryarchaeota. Using purified recombinant enzymes, we show that these ancestral forms have a nascent ability to decarboxylate kinetically less preferred amino acid substrates with low efficiency, and that product inhibition primarily affects preferred substrates. We also note a correlation between the presence of ancestral ODC and ornithine/arginine auxotrophy and link this with a known symbiotic dependence on exogenous ornithine produced by species using the arginine deiminase system. Finally, we show that ADC, ODC, and LDC activities emerged independently, in parallel, in the homologous AAT-fold ancestral and extended forms. The emergence of the same ODC, ADC, and LDC activities in the nonhomologous AR-fold suggests that polyamine biosynthesis may be inevitable.

Interactions between temperature and energy supply drive microbial communities in hydrothermal sediment

Temperature and bioavailable energy control the distribution of life on Earth, and interact with each other due to the dependency of biological energy requirements on temperature. Here we analyze how temperature-energy interactions structure sediment microbial communities in two hydrothermally active areas of Guaymas Basin. Sites from one area experience advective input of thermogenically produced electron donors by seepage from deeper layers, whereas sites from the other area are diffusion-dominated and electron donor-depleted. In both locations, Archaea dominate at temperatures >45 °C and Bacteria at temperatures <10 °C. Yet, at the phylum level and below, there are clear differences. Hot seep sites have high proportions of typical hydrothermal vent and hot spring taxa. By contrast, high-temperature sites without seepage harbor mainly novel taxa belonging to phyla that are widespread in cold subseafloor sediment. Our results suggest that in hydrothermal sediments temperature determines domain-level dominance, whereas temperature-energy interactions structure microbial communities at the phylum-level and below.

Lagostina et al. show that relative abundances of Bacteria and Archaea in sediments of Guaymas Basin, Gulf of California, are controlled by temperature, while energy flux explains microbial community structure at the phylum-level and below. Hot diffusion-dominated and energy-depleted sediments are dominated by taxa with relatives in cold subseafloor sediments, while hot sediments with high energy supply from fluid seepage are dominated by taxa also found at hydrothermal vents and in hot springs.

Prokaryotic and eukaryotic diversity in hydrothermal continental systems

The term extremophile was suggested more than 30 years ago and represents microorganisms that are capable of developing and living under extreme conditions, these conditions being particularly hostile to other types of microorganisms and to humankind. In terrestrial hydrothermal sites, like hot springs, "mud pools", solfataras, and geysers, the dominant extreme conditions are high temperature, low or high pH, and high levels of salinity. The diversity of microorganisms inhabiting these sites is determined by the conditions of the environment. Organisms belonging to the domains Archaea and Bacteria are more represented than the one belonging to Eukarya. Eukarya members tend to be less present because of their lower tolerance to higher temperatures, however, they perform important ecosystem processes when present. Both prokaryotes and eukaryotes have morphological and physical adaptations that allow them to colonize extreme environments. Microbial mats are complex associations of microorganisms that help the colonization of more extreme systems. In this review, a characterization of prokaryotic and eukaryotic organisms that populate terrestrial hydrothermal systems are made.

Microbiome structure and functional potential in permafrost soils of the Western Canadian Arctic

Substantial amounts of topsoil organic matter (OM) in Arctic Cryosols have been translocated by the process of cryoturbation into deeper soil horizons (cryoOM), reducing its decomposition. Recent Arctic warming deepens the Cryosols´ active layer, making more topsoil and cryoOM carbon accessible for microbial transformation. To quantify bacteria, archaea and selected microbial groups (methanogens - mcrA gene and diazotrophs - nifH gene) and to investigate bacterial and archaeal diversity, we collected 83 soil samples from four different soil horizons of three distinct tundra types located in Qikiqtaruk (Hershel Island, Western Canada). In general, the abundance of bacteria and diazotrophs decreased from topsoil to permafrost, but not for cryoOM. No such difference was observed for archaea and methanogens. CryoOM was enriched with oligotrophic (slow-growing microorganism) taxa capable of recalcitrant OM degradation. We found distinct microbial patterns in each tundra type: topsoil from wet-polygonal tundra had the lowest abundance of bacteria and diazotrophs, but the highest abundance of methanogens. Wet-polygonal tundra, therefore, represented a hotspot for methanogenesis. Oligotrophic and copiotrophic (fast-growing microorganism) genera of methanogens and diazotrophs were distinctly distributed in topsoil and cryoOM, resulting in different rates of nitrogen flux into these horizons affecting OM vulnerability and potential CO2 and CH4 release.

Enhanced production of methane in anaerobic water treatment as mediated by the immobilized fungi

Anaerobic digestion of organic waste and wastewater represents an attractive sustainable bio-technology to produce methane as an alternative to fossil energy. In response to improvement of methane production via enhancing methanogenesis, current strategies of the addition of external biological/non-biological materials have to confront either the loss of materials, high cost and/or possible destruction of the microbial community. Here, we report the first case of using immobilized fungi Aspergillus sydowii 8L-9-F02 to optimize the microbial community, achieving remarkable improvement of the methane production in both batch test (1.5 times) and continuous flow operation (1.13-1.31 times). The crucial role of fungi is associated with the stimulation of enrichment of Methanosaeta and Methanobacterium for methanogenesis from 28.2 to 67.4% as well as the improved activity of enzyme F420. Moreover, fungi also increase the content of extracellular polymeric substances, facilitating the formation of bio-aggregates. This work provides a new pathway to enhance methanogenesis during anaerobic digestion of wastewater by using fungi as bio-enhancer.

Variable sediment methane production in response to different source-associated sewer sediment types and hydrological patterns: Role of the sediment microbiome

Production of methane (CH₄), an essential anthropogenic greenhouse gas, from municipal sewer sediment is a problem deserving intensive attention. Based on long-term laboratory batch tests in conjunction with 16 s rRNA gene sequencing and metagenomics, this study provides the first detailed assessment of the variable sediment CH₄ production in response to different pollution source-associated sewer sediment types and hydrological patterns, while addressing the role of the sediment microbiome. The high CH₄-production capability of sanitary sewer sediment is shaped by enriched biologically active substrate and dominated by acetoclastic methanogenesis (genus Methanosaeta). Moreover, it involves syntrophic interactions among fermentation bacteria, hydrogen-producing acetogens and methanogens. Distinct source-associated microbial species, denitrifying bacteria and sulfate-reducing bacteria occur in storm sewer and illicit discharge-associated (IDA) storm sewer sediments. This reveals their insufficient microbial function capabilities to support efficient methanogenesis. Hydrogenotrophic methanogenesis (genus Methanobacterium) prevails in both these sediments. In this context, storm sewer sediment has an extremely low CH₄-production capability, while IDA storm sewer sediment still shows significant carbon emission through a possibly unique mechanism. Hydrological connections promote the sewer sediment biodegradability and CH₄-production capability. In contrast, hydrological disconnection facilitates the prevalence of acetoclastic methanogenesis, sulfate-reducing enzymes, denitrification enzymes and the sulfur-utilizing chemolithoautotrophic denitrifier, which drastically decreases CH₄ production. Turbulent suspension of sediments results in relative stagnation of methanogenesis. This work bridges the knowledge gap and will help to stimulate and guide the resolution of 'bottom-up' system-scale carbon budgets and GHG sources, as well as the target CH₄ abatement interventions.

Isolation of a member of the candidate phylum 'Atribacteria' reveals a unique cell membrane structure

A key feature that differentiates prokaryotic cells from eukaryotes is the absence of an intracellular membrane surrounding the chromosomal DNA. Here, we isolate a member of the ubiquitous, yet-to-be-cultivated phylum ‘Candidatus Atribacteria’ (also known as OP9) that has an intracytoplasmic membrane apparently surrounding the nucleoid. The isolate, RT761, is a subsurface-derived anaerobic bacterium that appears to have three lipid membrane-like layers, as shown by cryo-electron tomography. Our observations are consistent with a classical gram-negative structure with an additional intracytoplasmic membrane. However, further studies are needed to provide conclusive evidence for this unique intracellular structure. The RT761 genome encodes proteins with features that might be related to the complex cellular structure, including: N-terminal extensions in proteins involved in important processes (such as cell-division protein FtsZ); one of the highest percentages of transmembrane proteins among gram-negative bacteria; and predicted Sec-secreted proteins with unique signal peptides. Physiologically, RT761 primarily produces hydrogen for electron disposal during sugar degradation, and co-cultivation with a hydrogen-scavenging methanogen improves growth. We propose RT761 as a new species, Atribacter laminatus gen. nov. sp. nov. and a new phylum, Atribacterota phy. nov.

A key feature that differentiates prokaryotic cells from eukaryotes is the absence of an intracellular membrane surrounding the chromosomal DNA. Here, the authors isolate a member of the ubiquitous, yet-to-be-cultivated bacterial phylum ‘Candidatus Atribacteria’ that has an intracytoplasmic membrane apparently surrounding the nucleoid.

One or two membranes? Diderm Firmicutes challenge the Gram-positive/Gram-negative divide

How, when and why the transition between cell envelopes with one membrane (Gram-positives or monoderms) and two (Gram-negative or diderms) occurred in Bacteria is a key unanswered question in evolutionary biology. Different hypotheses have been put forward, suggesting that either the monoderm or the diderm phenotype is ancestral. The existence of diderm members in the classically monoderm Firmicutes challenges the Gram-positive/Gram-negative divide and provides a great opportunity to tackle the issue. In this review, we present current knowledge on the diversity of bacterial cell envelopes, including these atypical Firmicutes. We discuss how phylogenomic analysis supports the hypothesis that the diderm cell envelope architecture is an ancestral character in the Firmicutes, and that the monoderm phenotype in this phylum arose multiple times independently by loss of the outer membrane. Given the overwhelming distribution of diderm phenotypes with respect to monoderm ones, this scenario likely extends to the ancestor of all bacteria. Finally, we discuss the recent development of genetic tools for Veillonella parvula, a diderm Firmicute member of the human microbiome, which indicates it as an emerging new experimental model to investigate fundamental aspects of the diderm/monoderm transition.

Anaerobic digestion of purple phototrophic bacteria - The release step of the partition-release-recover concept

Purple phototrophic bacteria (PPB) have been proposed as a high-growth, assimilative option for wastewater treatment. The original partition-release-recover concept proposal requires their near complete digestion and release (and subsequent recovery) of energy and nutrients in an anaerobic digester. While the growth (partition) step has been extensively assessed, no work has been done on their anaerobic digestion characteristics (release). Continuous mesophilic (20d) and thermophilic (10d) digestion could achieve around 55% volatile solids degradation (VSD), with 35% (mesophilic) and 20% (thermophilic) nitrogen solubilisation. Post digestion (with/without pretreatment) could increase the VSD to 70% and nitrogen solubilisation to 43%. A number of pretreatment options were tested, with high temperature and sonication being relatively effective, and chemical treatment, and temperature phased digestion being relatively ineffective vs controls. Overall, anaerobic digestion of PPB results in substantial residual particulate material, with an increased nitrogen content, and avenues to effectively utilise this residue should be identified.

Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)

Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.

Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)

Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.

Long-term, selective production of caproate in an anaerobic membrane bioreactor

Fermentative caproate production from wastewater is attractive but is currently limited by the low product purity and concentration. In this work, continuous, selective production of caproate from acetate and ethanol, the common products of wastewater anaerobic fermentation, was achieved in an anaerobic membrane bioreactor (AnMBR). The reactor was continuously operated for over 522 days without need for chemical cleaning. With an ethanol-to-acetate ratio of 3.0, the effluent caproate concentration was 2.62 g/L on average and the caproate ratio in liquid products reached 74%. Further raising the influent ethanol content slightly increased the effluent caproate level but lowered the product selectivity and resulted in microbial inhibition. The Clostridia (the major caproate-producing bacteria) and Methanobacterium species (which consume hydrogen to alleviate microbial inhibition) was significantly enriched in the acclimated sludge. Our results imply a great potential of utilizing AnMBR to recover caproate from the effluent of wastewater acidogenic fermentation process.

Enrichment of specific microbial communities by optimum applied voltages for enhanced methane production by microbial electrosynthesis in anaerobic digestion

This study investigates the distribution of microbiome in microbial electrosynthesis systems at different applied voltages (0.5, 1.0, and 1.5 V) for methane production. Results revealed that more favorable conditions for methane production were observed with 1.0 V applied voltage. In Venn plots, the bioelectrodes at 1.0 V had higher numbers of unique operational taxonomic units compared to those at 0.5 and 1.5 V. Hierarchical cluster, non-metric multidimensional scaling, and principal component ordinate analyses revealed that the biocathode at 1.0 V clustered separately from the rest of the biofilms mainly because of the quantitative differences in the microbial distribution. Taxonomically, exoelectrogens (Geobacter spp.) dominated the bioanode at 1.0 V, while the syntrophic assemblages of hydrogen-producing bacteria (i.e., Bacteroidetes and Firmicutes) and hydrogen-consuming methanogens (i.e., Methanobacterium sp.) existed in the biocathode. These results suggest that the optimum applied voltage enriched specific microbial communities on the anode and cathode for enhanced methane production.

Applying potentials to conductive materials impairs High-loading anaerobic digestion performance by affecting direct interspecies electron transfer

In order to illustrate the impact that application of positive or negative potential to conductive materials can have on direct interspecies electron transfer (DIET) and reactor performance under high organic loading rates, three continuous laboratory-scale reactors with carbon-cloth electrodes poised at +0.7 V, -0.7 V (vs. Ag/AgCl) and no-potential were fed high concentrations of ethanol wastewater. While exoelectrogens and methanogens that are capable of DIET were significantly enriched in poised reactors, they performed worse than the non-current control. Volatile fatty acids (VFAs) accumulated more rapidly in the positively then negatively poised reactor, but neither could withstand high-loading rates. These results demonstrate that applying potential to conductive materials had a negative effect on anaerobic digestion under high-loading conditions.

Vertical stratification of bacteria and archaea in sediments of a small boreal humic lake

Although sediments of small boreal humic lakes are important carbon stores and greenhouse gas sources, the composition and structuring mechanisms of their microbial communities have remained understudied. We analyzed the vertical profiles of microbial biomass indicators (PLFAs, DNA and RNA) and the bacterial and archaeal community composition (sequencing of 16S rRNA gene amplicons and qPCR of mcrA) in sediment cores collected from a typical small boreal lake. While microbial biomass decreased with sediment depth, viable microbes (RNA and PLFA) were present all through the profiles. The vertical stratification patterns of the bacterial and archaeal communities resembled those in marine sediments with well-characterized groups (e.g. Methanomicrobia, Proteobacteria, Cyanobacteria, Bacteroidetes) dominating in the surface sediment and being replaced by poorly-known groups (e.g. Bathyarchaeota, Aminicenantes and Caldiserica) in the deeper layers. The results also suggested that, similar to marine systems, the deep bacterial and archaeal communities were predominantly assembled by selective survival of taxa able to persist in the low energy conditions. Methanotrophs were rare, further corroborating the role of these methanogen-rich sediments as important methane emitters. Based on their taxonomy, the deep-dwelling groups were putatively organo-heterotrophic, organo-autotrophic and/or acetogenic and thus may contribute to changes in the lake sediment carbon storage.

Colombian Andean thermal springs: reservoir of thermophilic anaerobic bacteria producing hydrolytic enzymes

Anaerobic cultivable microbial communities in thermal springs producing hydrolytic enzymes were studied. Thermal water samples from seven thermal springs located in the Andean volcanic belt, in the eastern and central mountain ranges of the Colombian Andes were used as inocula for the growth and isolation of thermophilic microorganisms using substrates such as starch, gelatin, xylan, cellulose, Tween 80, olive oil, peptone and casamino acids. These springs differed in temperature (50-70 °C) and pH (6.5-7.5). The predominant ion in eastern mountain range thermal springs was sulphate, whereas that in central mountain range springs was bicarbonate. A total of 40 anaerobic thermophilic bacterial strains that belonged to the genera Thermoanaerobacter, Caloramator, Anoxybacillus, Caloranaerobacter, Desulfomicrobium, Geotoga, Hydrogenophilus, Desulfacinum and Thermoanaerobacterium were isolated. To investigate the metabolic potential of these isolates, selected strains were analysed for enzymatic activities to identify strains than can produce hydrolytic enzymes. We demonstrated that these thermal springs contained diverse microbial populations of anaerobic thermophilic comprising different metabolic groups of bacteria including strains belonging to the genera Thermoanaerobacter, Caloramator, Anoxybacillus, Caloranaerobacter, Desulfomicrobium, Geotoga, Hydrogenophilus, Desulfacinum and Thermoanaerobacterium with amylases, proteases, lipases, esterases, xylanases and pectinases; therefore, the strains represent a promising source of enzymes with biotechnological potential.

Changes in the Substrate Source Reveal Novel Interactions in the Sediment-Derived Methanogenic Microbial Community

Methanogenesis occurs in many natural environments and is used in biotechnology for biogas production. The efficiency of methane production depends on the microbiome structure that determines interspecies electron transfer. In this research, the microbial community retrieved from mining subsidence reservoir sediment was used to establish enrichment cultures on media containing different carbon sources (tryptone, yeast extract, acetate, CO₂/H₂). The microbiome composition and methane production rate of the cultures were screened as a function of the substrate and transition stage. The relationships between the microorganisms involved in methane formation were the major focus of this study. Methanogenic consortia were identified by next generation sequencing (NGS) and functional genes connected with organic matter transformation were predicted using the PICRUSt approach and annotated in the KEGG. The methane production rate (exceeding 12.8 mg CH₄ L⁻¹ d⁻¹) was highest in the culture grown with tryptone, yeast extract, and CO₂/H_2. The analysis of communities that developed on various carbon sources casts new light on the ecophysiology of the recently described bacterial phylum Caldiserica and methanogenic Archaea representing the genera Methanomassiliicoccus and Methanothrix. Furthermore, it is hypothesized that representatives of Caldiserica may support hydrogenotrophic methanogenesis.

Probing the geological source and biological fate of hydrogen in Yellowstone hot springs

Hydrogen (H₂ ) is enriched in hot springs and can support microbial primary production. Using a series of geochemical proxies, a model to describe variable H₂ concentrations in Yellowstone National Park (YNP) hot springs is presented. Interaction between water and crustal iron minerals yields H₂ that partition into the vapour phase during decompressional boiling of ascending hydrothermal fluids. Variable vapour input leads to differences in H₂ concentration among springs. Analysis of 50 metagenomes from a variety of YNP springs reveals that genes encoding oxidative hydrogenases are enriched in communities inhabiting springs sourced with vapour-phase gas. Three springs in the Smokejumper (SJ) area of YNP that are sourced with vapour-phase gas and with the most H₂ in YNP were examined to determine the fate of H₂ . SJ3 had the most H₂ , the most 16S rRNA gene templates and the greatest abundance of culturable hydrogenotrophic and autotrophic cells of the three springs. Metagenomics and transcriptomics of SJ3 reveal a diverse community comprised of abundant populations expressing genes involved in H₂ oxidation and carbon dioxide fixation. These observations suggest a link between geologic processes that generate and source H₂ to hot springs and the distribution of organisms that use H₂ to generate energy.

The microbiota profile and transcriptome analysis of immune response during metamorphosis stages in orange spotted grouper (Epinephelus coioides)

Metamorphosis is a transformation process in larval development associated with changes in morphological and physiological features, including the immune system. The gastrointestinal tract harbors a plethora of bacteria, which might affect the digestion and absorption of nutrients, immunity, and gut-brain crosstalk in the host. In this study, we have performed metagenomic and transcriptomic analyses on the intestines of grouper at the pre-, mid- and post-metamorphosis stages. The sequencing data of 16S rRNA gene showed drastic changes in the microbial communities at different developmental stages. The transcriptomic data revealed that the leukocyte transendothelial migration and the phagosome pathways might play important roles in mediating immunity in grouper at the three developmental stages. This information will increase our understanding of the metamorphosis process in grouper larvae, and shed light on the development of antimicrobial strategy during larval development.

Mixing of meteoric and geothermal fluids supports hyperdiverse chemosynthetic hydrothermal communities

Little is known of how mixing of meteoric and geothermal fluids supports biodiversity in non-photosynthetic ecosystems. Here, we use metagenomic sequencing to investigate a chemosynthetic microbial community in a hot spring (SJ3) of Yellowstone National Park that exhibits geochemistry consistent with mixing of a reduced volcanic gas-influenced end member with an oxidized near-surface meteoric end member. SJ3 hosts an exceptionally diverse community with representatives from ~50% of known higher-order archaeal and bacterial lineages, including several divergent deep-branching lineages. A comparison of functional potential with other available chemosynthetic community metagenomes reveals similarly high diversity and functional potentials (i.e., incorporation of electron donors supplied by volcanic gases) in springs sourced by mixed fluids. Further, numerous closely related SJ3 populations harbor differentiated metabolisms that may function to minimize niche overlap, further increasing endemic diversity. We suggest that dynamic mixing of waters generated by subsurface and near-surface geological processes may play a key role in the generation and maintenance of chemosynthetic biodiversity in hydrothermal and other similar environments.

Chemosynthetic microbial communities in hydrothermal environments receiving meteoric and geothermal fluids are understudied. Here, Colman et al. use metagenomics to study one such community from a hot spring at Yellowstone National Park, revealing exceptional biodiversity and unique functional potential.

Free nitrous acid promotes hydrogen production from dark fermentation of waste activated sludge

Simultaneous sludge fermentation and nitrite removal is an effective approach to enhance nutrient removal from low carbon-wastewater. It was found in this work that the presence of nitrite largely promoted hydrogen production from acidic fermentation of waste activated sludge (WAS). The results showed that with an increase of nitrite from 0 to 250 mg/L, the maximal hydrogen yield increased from 8.5 to 15.0 mL/g VSS at pH 5.5 fermentation and 8.1-13.0 mL/g VSS at pH 6 fermentation. However, the maximal hydrogen yield from WAS fermentation at pH 8 remained almost constant (2.9-3.7 mL/g VSS) when nitrite was in the range of 0-250 mg/L. Further analyses revealed that free nitrous acid (FNA) rather than nitrite was the major contributor to the promotion of hydrogen yield. The mechanism investigations showed that FNA not only accelerated the disruption of sludge cells but also promoted the biodegradability of organics released, thereby provided more biodegradable substrates for subsequent hydrogen production. Although FNA inhibited activities of all microbes involved in the anaerobic fermentation, its inhibitions to hydrogen consumers were much severer than those to hydrolytic microorganisms and hydrogen producers. Further investigations with microbial community showed that FNA increased the abundances of hydrogen producers (e.g., Citrobacter sp.) and denitrifiers (e.g., Dechloromonas sp.), but reduced the abundances of hydrogen consumers (e.g., Clostridium_aceticum). This work demonstrated for the first time that FNA in WAS fermentation systems enhanced hydrogen production. The findings obtained expand the application field of FNA and may provide supports for sustainable operation of wastewater treatment plants.

Response of environmental variables and microbial community to sodium percarbonate addition to contaminated sediment

Sodium percarbonate (SPC) is a common reagent used for in situ remediation of contaminated soil. Current studies focus on the effects of SPC on pollutant removal; however, a knowledge gap exists for the biochemical process following SPC addition. In this study, a microcosm batch experiment was conducted to investigate the residual effect caused by different doses of SPC addition on native microbial communities, as well as on the environmental variables of contaminated sediments. The obtained results showed that the more SPC was added, the more dissolved matters were generated and the oxidation-reduction potential was lowered. Furthermore, the metabolic activities of the microbial community were enhanced and the microbial community structure responded differently to different SPC doses: the microbes that increased at high SPC dose mainly belonged to the phylum Firmicutes, the class Clostridia, and the genera Petrimonas and Proteiniclasticum. The microbes that increased at medium SPC dose mainly belonged to the class Alphaproteobacteria and the genus Brevundimonas. In contrast, vulnerable microbes mainly belonged to the phylum Acidobacteria, the class Caldisericia, Holophagae, and the genus Sulfuricurvum. Microbes capable of fermentation, ureolysis, and chemohetrotrophy increased. These results indicate that SPC addition could indirectly provide both electron acceptors and donors, thus improving the metabolic activities of the microorganisms in the contaminated sediment. Furthermore, the utilized SPC dose should be considered to achieve the optimal benefit for in situ remediation. This study forms a valuable reference for the application of SPC in ecological engineering.

Biogeochemical probing of microbial communities in a basalt-hosted hot spring at Kverkfjöll volcano, Iceland

We investigated bacterial and archaeal communities along an ice-fed surficial hot spring at Kverkfjöll volcano-a partially ice-covered basaltic volcano at Vatnajökull glacier, Iceland, using biomolecular (16S rRNA, apsA, mcrA, amoA, nifH genes) and stable isotope techniques. The hot spring environment is characterized by high temperatures and low dissolved oxygen concentrations at the source (68°C and <1 mg/L (±0.1%)) changing to lower temperatures and higher dissolved oxygen downstream (34.7°C and 5.9 mg/L), with sulfate the dominant anion (225 mg/L at the source). Sediments are comprised of detrital basalt, low-temperature alteration phases and pyrite, with <0.4 wt. % total organic carbon (TOC). 16S rRNA gene profiles reveal that organisms affiliated with Hydrogenobaculum (54%-87% bacterial population) and Thermoproteales (35%-63% archaeal population) dominate the micro-oxic hot spring source, while sulfur-oxidizing archaea (Sulfolobales, 57%-82%), and putative sulfur-oxidizing and heterotrophic bacterial groups dominate oxic downstream environments. The δ¹³ C_org (‰ V-PDB) values for sediment TOC and microbial biomass range from -9.4‰ at the spring's source decreasing to -12.6‰ downstream. A reverse effect isotope fractionation of ~3‰ between sediment sulfide (δ³⁴ S ~0‰) and dissolved water sulfate (δ³⁴ S +3.2‰), and δ¹⁸ O values of ~ -5.3‰ suggest pyrite forms abiogenically from volcanic sulfide, followed by abiogenic and microbial oxidation. These environments represent an unexplored surficial geothermal environment analogous to transient volcanogenic habitats during putative "snowball Earth" scenarios and volcano-ice geothermal environments on Mars.

Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration

The decomposition of large stocks of soil organic carbon in thawing permafrost might depend on more than climate change-induced temperature increases: indirect effects of thawing via altered bacterial community structure (BCS) or rooting patterns are largely unexplored. We used a 10-year in situ permafrost thaw experiment and aerobic incubations to investigate alterations in BCS and potential respiration at different depths, and the extent to which they are related with each other and with root density. Active layer and permafrost BCS strongly differed, and the BCS in formerly frozen soils (below the natural thawfront) converged under induced deep thaw to strongly resemble the active layer BCS, possibly as a result of colonization by overlying microorganisms. Overall, respiration rates decreased with depth and soils showed lower potential respiration when subjected to deeper thaw, which we attributed to gradual labile carbon pool depletion. Despite deeper rooting under induced deep thaw, root density measurements did not improve soil chemistry-based models of potential respiration. However, BCS explained an additional unique portion of variation in respiration, particularly when accounting for differences in organic matter content. Our results suggest that by measuring bacterial community composition, we can improve both our understanding and the modeling of the permafrost carbon feedback.

Methanogenic and Sulfate-Reducing Activities in a Hypersaline Microbial Mat and Associated Microbial Diversity

Methanogenesis and sulfate reduction are important microbial processes in hypersaline environments. However, key aspects determining substrate competition between these microbial processes have not been well documented. We evaluated competitive and non-competitive substrates for stimulation of both processes through microcosm experiments of hypersaline microbial mat samples from Guerrero Negro, Baja California Sur, Mexico, and we assessed the effect of these substrates on the microbial community composition. Methylotrophic methanogenesis evidenced by sequences belonging to methanogens of the family Methanosarcinaceae was found as the dominant methanogenic pathway in the studied hypersaline microbial mat. Nevertheless, our results showed that incubations supplemented with acetate and lactate, performed in absence of sulfate, also produced methane after 40 days of incubation, apparently driven by hydrogenotrophic methanogens affiliated to the family Methanomicrobiaceae. Sulfate reduction was mainly stimulated by addition of acetate and lactate; however, after 40 days of incubation, an increase of the H₂S concentrations in microcosms amended with trimethylamine and methanol was also observed, suggesting that these substrates are putatively used for sulfate reduction. Moreover, 16S rRNA gene sequencing analysis showed remarkable differences in the microbial community composition among experimental treatments. In the analyzed sample amended with acetate, sulfate-reducing bacteria (SRB) belonging to the family Desulfobacteraceae were dominant, while members of Desulfohalobiaceae, Desulfomicrobiaceae, and Desulfovibrionaceae were found in the incubation with lactate. Additionally, we detected an unexpected high abundance of unclassified Hydrogenedentes (near 25%) in almost all the experimental treatments. This study contributes to better understand methanogenic and sulfate-reducing activities, which play an important role in the functioning of hypersaline environments.