Prolixibacter bellariivorans gen. nov., sp. nov., a sugar-fermenting, psychrotolerant anaerobe of the phylum Bacteroidetes, isolated from a marine-sediment fuel cell

Impact of Silver and Copper Oxide Nanoparticles on Anaerobic Digestion of Sludge and Bacterial Community Structure

The effect of metal nanoparticles on the anaerobic digestion of sludge and the sludge bacterial community are still not well-understood, and both improvements and inhibitions have been reported. This study investigated the impact of 2, 10, and 30 mg/g TS silver and copper oxide nanoparticles (AgNPs and CuONPs) on the mesophilic anaerobic digestion of sludge and the bacterial community structure. The reactors were monitored for changes in tCOD, sCOD, TS, VS, biogas generation, and cell viability. Also, the relative abundance and taxonomic distribution of the bacterial communities were analyzed at the phylum and genus levels, including the genera involved in anaerobic digestion. Both AgNPs and CuONPs exhibited some inhibition on anaerobic digestion of sludge and biogas generation, and the inhibition was more evident at higher concentrations. CuONPs had a stronger inhibitory effect compared to AgNPs. After the introduction of AgNPs and CuONPs, cell viability initially decreased over the first two weeks but recovered after that. At high concentrations, AgNPs and CuONPs decreased the overall bacterial diversity, and inhibited the dominant bacterial species, allowing those in less abundance to flourish. The relative abundance of the bacteria responsible for hydrolysis and acidogenesis increased and the relative abundance of acetogenic bacteria decreased with higher AgNP and CuONP concentrations. The majority of the parameters measured for monitoring the anaerobic digestion performance and bacterial community were not statistically significant at 2 mg/g TS of AgNPs and CuONPs, which represents naturally present concentrations in wastewater sludge that are below the USEPA ceiling concentration limits.

Halosquirtibacter laminarini gen. nov., sp. nov. and Halosquirtibacter xylanolyticus sp. nov., marine anaerobic laminarin and xylan degraders in the phylum Bacteroidota

The bacterial group of the phylum Bacteroidota greatly contributes to the global carbon cycle in marine ecosystems through its specialized ability to degrade marine polysaccharides. In this study, it is proposed that two novel facultative anaerobic strains, DS1-an-13321T and DS1-an-2312T, which were isolated from a sea squirt, represent a novel genus, Halosquirtibacter, with two novel species in the family Prolixibacteraceae. The 16S rRNA sequence similarities of these two strains were 91.26% and 91.37%, respectively, against Puteibacter caeruleilacunae JC036T, which is the closest recognized neighbor. The complete genomes of strains DS1-an-13321T and DS1-an-2312T each consisted of a single circular chromosome with a size of 4.47 and 5.19 Mb, respectively. The average amino acid identity and the percentage of conserved proteins against the type species of the genera in the family Prolixibacteraceae ranged from 48.33 to 52.35% and 28.34-37.37%, respectively, which are lower than the threshold for genus demarcation. Strains DS1-an-13321T and DS1-an-2312T could grow on galactose, glucose, maltose, lactose, sucrose, laminarin, and starch, and only DS1-an-2312T could grow on xylose and xylan under fermentation conditions. These strains produced acetic acid and propionic acid as the major fermentation products. Genome mining of the genomes of the two strains revealed 27 and 34 polysaccharide utilization loci, which included 155 and 249 carbohydrate-active enzymes (CAZymes), covering 57 and 65 CAZymes families, respectively. The laminarin-degrading enzymes in both strains were cell-associated, and showed exo-hydrolytic activity releasing glucose as a major product. The xylan-degrading enzymes of strain DS1-an-2312T was also cell-associated, and had endo-hydrolytic activities, releasing xylotriose and xylotetraose as major products. The evidence from phenotypic, biochemical, chemotaxonomic, and genomic characteristics supported the proposal of a novel genus with two novel species in the family Prolixibacteraceae, for which the names Halosquirtibacter laminarini gen. nov., sp. nov. and Halosquirtibacter xylanolyticus sp. nov. are proposed. The type strain of Halosquirtibacter laminarini is DS1-an-13321T (= KCTC 25031T = DSM 115329T) and the type strain of Halosquirtibacter xylanolyticus is DS1-an-2312T (= KCTC 25032T = DSM 115328T).

Incorporating saline microalgae biomass in anaerobic digester treating sewage sludge: Impact on performance and microbial populations

The aim of this study was to acclimate anaerobic prokaryotes to saline microalgae biomass. Semi-continuous experiments were conducted using two 1.5 L mesophilic reactors for 10 weeks, (hydraulic retention time of 21 days). The first reactor was solely fed with sewage sludge (control), while the second received a mixture of sewage sludge and microalgal biomass (80/20 %w/w) cultivated at 70 g·L-1 salinity. The in-reactor salinity reached after the acclimation phase was 14 g·L-1. Biomethane production was comparable between the control and acclimated reactors (205 ± 29 NmLMethane·gVolatileSolids-1). Salinity tolerance assessment of methanogenic archaea revealed that salinity causing 50% inhibition of methane production increased from 10 to 27 g·L-1 after acclimation. Microbial diversity analyses revealed notable changes in methanogenic archaea populations during co-digestion of saline microalgae biomass, particularly methylotrophic (+27%) and acetotrophic (-26%) methanogens. This study has highlighted the possibility of treating efficiently saline microalgae in co-digestion with sewage sludge in future industrial biogas plants.

Gaoshiqia sediminis gen. nov., sp. nov., isolated from coastal sediment

A Gram-stain-negative, facultative anaerobic, motile, rod-shaped and orange bacterium, designated A06^T, was obtained off the coast of Weihai, PR China. Cells were 0.4-0.5×0.6-1.0 µm in size. Strain A06^T grew at 20-40 °C (optimum, 33 °C), at pH 6.0-8.0 (optimum, pH 6.5-7.0) and in the presence of 0-8 % NaCl (w/v) (optimum, 2 %). Cells were oxidase and catalase positive. Menaquinone-7 was detected as the major respiratory quinone. The dominant cellular fatty acids were identified as C_15:0 2-OH, iso-C_15:0, anteiso-C_15:0 and iso-C_15:1  ω6c. The DNA G+C content of strain A06^T was 46.1 mol%. The polar lipids were phosphatidylethanolamine, one aminolipid, one glycolipid and three unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain A06^T is a member of the family Prolixibacteraceae and exhibited the highest sequence similarity to Mangrovibacterium diazotrophicum DSM 27148^T (94.3 %). Based on its phylogenetic and phenotypic characteristics, strain A06^T is considered to represent a novel genus in the family Prolixibacteraceae, for which the name Gaoshiqia gen. nov. is proposed. The type species is Gaoshiqia sediminis sp. nov., with type strain A06^T (=KCTC 92029^T=MCCC 1H00491^T). The identification and acquisition of microbial species and genes in sediments will help broaden the understanding of microbial resources and lay a foundation for its application in biotechnology. Strain A06^T uses an enrichment method, so the isolation of strain A06^T is of great significance to the enrichment of marine microbial resources.

The Epibiotic Microbiota of Wild Caribbean Sea Urchin Spines Is Species Specific

Caribbean sea urchins are marine invertebrates that have experienced a decline over the years. Studies on sea urchins have focused primarily on the microbiome of the coelomic fluid or the gut microbiota. In this study, the epibiota community associated with four wild Caribbean sea urchin species, Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum, was characterized for the first time. Using 57 sea urchin animal samples, we evaluated the influence of animal species, trophic niches, and geographical location on the composition of the epibiotic microbiota. We found significant differences in the bacterial biota among species and trophic niches, but not among geographical locations. L. variegatus exhibited the highest alpha diversity with high dominance of Fusobacteria, Planctomycetes, and Cyanobacteria, whereas T. ventricosus and D. antillarum were dominated by Firmicutes. T. ventricosus inhabiting the seagrass biotope dominated by Thalassia testudinum meadows had mostly Endozoicomonas. In contrast, samples located in the reef (dominated by corals and other reef builders) had a higher abundance of Kistimonas and Photobacterium. Our findings confirm that the epibiotic microbiota is species-specific, but also niche-dependent, revealing the trophic networks emerging from the organic matter being recycled in the seagrass and reef niches. As echinoids are important grazers of benthic communities, their microbiota will likely influence ecosystem processes.

Copper removal and elemental sulfur recovery from fracturing flowback water in a microbial fuel cell with an extra electrochemical anode

Fracturing flowback water (FFW) from the shale gas exploitation resulted in environmental burden. FFW could be treated by a microbial fuel cell (MFC), but the challenge for the precipitation of ultrafine particles due to the supersaturation of sulfide remains to be addressed. Herein, we reported a Dual-anode MFC (DA-MFC), in which the FFW remediation and elemental sulfur recovery could be performed by regulating potential of the electrochemical anode. The removal of COD and sulfate was 70.0 ± 1.2% and 75.5 ± 0.4% in DA-MFCs by controlling potential at -0.1 V (vs. SHE) for 36 h. Meanwhile, the efficiency of copper removal and elemental sulfur recovery was up to 99.9 ± 0.5% and 75.6 ± 1.8%, respectively, which was attributed by the electrochemical oxidation of sulfide to elemental sulfur. Trichococcus, unclassified Prolixibacteraceae and unclassified Cloacimonadales enriched on the bioanodes of DA-MFCs were sensitive to potential regulation and favorable for degrading complex organics. UnclassifiedSynergistaceae, Desulfobacterium, Desulfovibrio, unclassified bacteria and Syner-01 was conducive to sulfate removal. Moreover, the elimination of Azoarcus due to potential regulation suppressed the biological oxidation of sulfide. Thus, organics were efficiently removed through the biological oxidation and sulfate reduction on bioanode, the copper ions were combined with the sulfide from sulfate reduction to precipitate effectively, and then the excessive sulfide in the system was converted into elemental sulfur attached on the electrochemical anode. The results provide new sights on bio-electrochemical technology for treatment of wastewater containing complex organics, heavy metals and sulfates.

Laboratory-Controlled Experiments Reveal Microbial Community Shifts during Sediment Resuspension Events

In freshwater ecosystems, dynamic hydraulic events (floods or dam maintenance) lead to sediment resuspension and mixing with waters of different composition. Microbial communities living in the sediments play a major role in these leaching events, contributing to organic matter degradation and the release of trace elements. However, the dynamics of community diversity are seldom studied in the context of ecological studies. Therefore, we carried out laboratory-induced leaching experiments, using sediments from the Villerest dam reservoir (Villerest, France). To assess whole microbial community diversity, we sequenced the archaeal and bacterial 16S rRNA genes using Illumina MiSeq. Our results suggest that the degree of dissolved oxygen found in the water during these resuspension episodes influenced community dynamics, with anoxic waters leading to drastic shifts in sedimentary communities compared to oxic waters. Furthermore, the release of microbial cells from sediments to the water column were more favorable to water colonization when events were caused by oxic waters. Most of the bacteria found in the sediments were chemoorganotrophs and most of the archaea were methanogens. Methylotrophic, as well as archaeal, and bacterial chemoorganotrophs were detected in the leachate samples. These results also show that organic matter degradation occurred, likely participating in carbonate dissolution and the release of trace elements during freshwater resuspension events.

Mechanisms Driving Microbial Community Composition in Anaerobic Co-Digestion of Waste-Activated Sewage Sludge

Anaerobic co-digestion (Co-AD) is used to increase the effectiveness of anaerobic digestion (AD) using local “wastes”, adding economic and environmental benefits. Since system stability is of existential importance for the operation of wastewater treatment plants, thorough testing of potential co-substrates and their effects on the respective community and system performance is crucial for understanding and utilizing Co-AD to its best capacity. Food waste (FW) and canola lecithin (CL) were tested in mesophilic, lab-scale, semi-continuous reactors over a duration of 120 days with stepwise increased substrate addition. Key performance indicators (biogas, total/volatile solids, fatty acids) were monitored and combined with 16S-rRNA amplicon sequencing to assess the impact of co-substrate addition on reactor performance and microbial community composition (MCC). Additionally, the latter was then compared with natural shifts occurring in the wastewater treatment plant (WWTP, source) at the same time. An almost linear increase in biogas production with both co-substrates at an approximate 1:1 ratio with the organic loading rate (OLR) was observed. The MCCs in both experiments were mostly stable, but also prone to drift over time. The FW experiment MCC more closely resembled the original WWTP community and the observed shifts indicated high levels of functional redundancy. Exclusive to the CL co-substrate, a clear selection for a few operational taxonomic units (OTUs) was observed. There was little evidence for a persistent invasion and establishment of microorganisms from typical primary substrates into the stable resident community of the reactors, which is in line with earlier findings that suggested that the inoculum and history mostly define the MCC. However, external factors may still tip the scales in favor of a few r-strategists (e.g., Prolixibacter) in an environment that otherwise favors K-strategists, which may in fact also be recruited from the primary substrate (Trichococcus). In our study, specialization and diversity loss were also observed in response to the addition of the highly specialized CL, which in turn, may have adverse effects on the system’s stability and reduced resilience and recovery.

Sulfidogenic fluidized-bed bioreactor kinetics for co-treatment of hospital wastewater and acid mine drainage

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Bioremediation process for acidic mine water co-treatment with hospital wastewater.

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Metal precipitation reached 98% and soluble concentrations of Fe and Zn were less than 0.1 mg/l.

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SO₄²⁻ removal was above 90% in the sulfidogenic bioreactor.

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Naproxen, ibuprofen, ketoprofen, and diclofenac partially removed during the co-treatment process.

A passive co-treatment of acid mine drainage and hospital wastewater previously demonstrated a promising bioremediation viable approach for both toxic streams. The study of inhibition kinetics and microbial communities is essential to understand better the diverse species and the reaction mechanisms within the system. The kinetics and microbiology diversity in the sulfidogenic fluidized-bed reactor (at 30 °C) for co-treatment of hospital wastewater and metal-containing acidic water were examined. The alkalinity from organic oxidation raised the pH of the effluent from 2.3 to 6.1–8.2. Michaelis-Menten modeling yielded (K_m =7.3 mg/l, V_max = 0.12 mg/l min⁻¹) in the batch bioreactor treatment using sulfate-reducing bacteria. For COD oxidation, the dissolved sulfide inhibition constant (K_i) was 3.6 mg/l, and the K_i value for H₂S was 9 mg/l. The dominant species in the treatment process belong to the Proteobacteria group (especially Deltaproteobacteria). The ibuprofen and diclofenac compounds achieved the highest removal rates in the bioreactor of 58.6% and 52.3%, respectively; while, ketoprofen and naproxen of 41.9% and 46.6%, respectively. The findings in COD kinetics, sulfate-reducing bacteria abundance, and selected pharmaceutical concentration reduction provide insight into this co-treatment process's capability.

Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins

Sea urchins play a critical role in marine ecosystems, as they actively participate in maintaining the balance between coral and algae. We performed the first in-depth survey of the microbiota associated with four free-living populations of Caribbean sea urchins: Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum. We compared the influence of the collection site, echinoid species and trophic niche to the composition of the microbiota. This dataset provides a comprehensive overview to date, of the bacterial communities and their ecological relevance associated with sea urchins in their natural environments. A total of sixty-samples, including surrounding reef water and seagrass leaves underwent 16S rRNA gene sequencing (V4 region) and high-quality reads were analyzed with standard bioinformatic approaches. While water and seagrass were dominated by Cyanobacteria such as Prochlorococcus and Rivularia respectively, echinoid gut samples had dominant Bacteroidetes, Proteobacteria and Fusobacteria. Propionigenium was dominant across all species' guts, revealing a host-associated composition likely responsive to the digestive process of the animals. Beta-diversity analyses showed significant differences in community composition among the three collection sites, animal species, and trophic niches. Alpha diversity was significantly higher among L. variegatus samples compared to the other species. L. variegatus also displayed an increased abundance of Planctomycetes and Cyanobacterial OTUs. The bacterial community of this herbivorous echinoid reflected similarities to the microfilm community found on Thalassia testudinum leaves; a very abundant seagrass and its main food resource. The results of this study elaborate on the microbial ecology of four important Caribbean echinoids, confirming that selection on the microbial community is trophic-niche dependent.

Temperature differently affected methanogenic pathways and microbial communities in sub-Antarctic freshwater ecosystems

Freshwater ecosystems are responsible for an important part of the methane (CH₄) emissions which are likely to change with global warming. This study aims to evaluate temperature-induced (from 5 to 20 °C) changes on microbial community structure and methanogenic pathways in five sub-Antarctic lake sediments from Magallanes strait to Cape Horn, Chile. We combined in situ CH₄ flux measurements, CH₄ production rates (MPRs), gene abundance quantification and microbial community structure analysis (metabarcoding of the 16S rRNA gene). Under unamended conditions, a temperature increase of 5 °C doubled MPR while microbial community structure was not affected. Stimulation of methanogenesis by methanogenic precursors as acetate and H₂/CO₂, resulted in an increase of MPRs up to 127-fold and 19-fold, respectively, as well as an enrichment of mcrA-carriers strikingly stronger under acetate amendment. At low temperatures, H₂/CO₂-derived MPRs were considerably lower (down to 160-fold lower) than the acetate-derived MPRs, but the contribution of hydrogenotrophic methanogenesis increased with temperature. Temperature dependence of MPRs was significantly higher in incubations spiked with H₂/CO₂ (c. 1.9 eV) compared to incubations spiked with acetate or unamended (c. 0.8 eV). Temperature was not found to shape the total microbial community structure, that rather exhibited a site-specific variability among the studied lakes. However, the methanogenic archaeal community structure was driven by amended methanogenic precursors with a dominance of Methanobacterium in H₂/CO₂-based incubations and Methanosarcina in acetate-based incubations. We also suggested the importance of acetogenic H₂-production outcompeting hydrogenotrohic methanogenesis especially at low temperatures, further supported by homoacetogen proportion in the microcosm communities. The combination of in situ-, and laboratory-based measurements and molecular approaches indicates that the hydrogenotrophic pathway may become more important with increasing temperatures than the acetoclastic pathway. In a continuously warming environment driven by climate change, such issues are crucial and may receive more attention.

Nitrite as a causal factor for nitrate-dependent anaerobic corrosion of metallic iron induced by Prolixibacter strains

Microbially influenced corrosion (MIC) may contribute significantly to overall corrosion risks, especially in the gas and petroleum industries. In this study, we isolated four Prolixibacter strains, which belong to the phylum Bacteroidetes, and examined their nitrate respiration- and Fe0 -corroding activities, together with two previously isolated Prolixibacter strains. Four of the six Prolixibacter strains reduced nitrate under anaerobic conditions, while the other two strains did not. The anaerobic growth of the four nitrate-reducing strains was enhanced by nitrate, which was not observed in the two strains unable to reduce nitrate. When the nitrate-reducing strains were grown anaerobically in the presence of Fe0 or carbon steel, the corrosion of the materials was enhanced by more than 20-fold compared to that in aseptic controls. This enhancement was not observed in cultures of the strains unable to reduce nitrate. The oxidation of Fe0 in the anaerobic cultures of nitrate-reducing strains occurred concomitantly with the formation of nitrite. Since nitrite chemically oxidized Fe0 under anaerobic and aseptic conditions, the corrosion of Fe0 - and carbon steel by the nitrate-reducing Prolixibacter strains was deduced to be mainly enhanced via the biological reduction of nitrate to nitrite, followed by the chemical oxidation of Fe0 to Fe2+ and Fe3+ coupled to the reduction of nitrite.

Functional Interrelationships of Microorganisms in Iron-Based Anaerobic Wastewater Treatment

This study explicated the functional activities of microorganisms and their interrelationships under four previously reported iron reducing conditions to identify critical factors that governed the performance of these novel iron-dosed anaerobic biological wastewater treatment processes. Various iron-reducing bacteria (FeRB) and sulfate reducing bacteria (SRB) were identified as the predominant species that concurrently facilitated organics oxidation and the main contributors to removal of organics. The high organic contents of wastewater provided sufficient electron donors for active growth of both FeRB and SRB. In addition to the organic content, Fe (III) and sulfate concentrations (expressed by Fe/S ratio) were found to play a significant role in regulating the microbial abundance and functional activities. Various fermentative bacteria contributed to this FeRB-SRB synergy by fermenting larger organic compounds to smaller compounds, which were subsequently used by FeRB and SRB. Feammox (ferric reduction coupled to ammonium oxidation) bacterium was identified in the bioreactor fed with wastewater containing ammonium. Organic substrate level was a critical factor that regulated the competitive relationship between heterotrophic FeRB and Feammox bacteria. There were evidences that suggested a synergistic relationship between FeRB and nitrogen-fixing bacteria (NFB), where ferric iron and organics concentrations both promoted microbial activities of FeRB and NFB. A concept model was developed to illustrate the identified functional interrelationships and their governing factors for further development of the iron-based wastewater treatment systems.

Students in a Course-Based Undergraduate Research Experience Course Discovered Dramatic Changes in the Bacterial Community Composition Between Summer and Winter Lake Samples

Course-based undergraduate research experience (CURE) courses incorporate high-impact pedagogies that have been shown to increase undergraduate retention among underrepresented minorities and women. As part of the Building Infrastructure Leading to Diversity program at the University of Detroit Mercy, a CURE metagenomics course was established in the winter of 2019. Students investigated the bacterial community composition in a eutrophic cove in Lake Saint Clair (Harrison Township, MI, United States) from water samples taken in the summer and winter. The students created 16S rRNA libraries that were sequenced using next-generation sequencing technology. They used a public web-based supercomputing resource to process their raw sequencing data and web-based tools to perform advanced statistical analysis. The students discovered that the most common operational taxonomic unit, representing 31% of the prokaryotic sequences in both summer and winter samples, corresponded to an organism that belongs to a previously unidentified phylum. This result showed the students the power of metagenomics because the approach was able to detect unclassified organisms. Principal Coordinates Analysis of Bray-Curtis dissimilarity index data showed that the winter community was distinct from the summer community [Analysis of Similarities (ANOSIM) r = 0.59829, n = 18, and p < 0.001]. Dendrograms based on hierarchically clustered Pearson correlation coefficients of phyla were divided into a winter clade and a summer clade. The conclusion is that the winter bacterial population was fundamentally different from the summer population, even though the samples were taken from the same locations in a protected cove. Because of the small class sizes, qualitative as well as statistical methods were used to evaluate the course's impact on student attitudes. Results from the Laboratory Course Assessment Survey showed that most of the respondents felt they were contributing to scientific knowledge and the course fostered student collaboration. The majority of respondents agreed or strongly agreed that the course incorporated iteration aspects of scientific investigations, such as repeating procedures to fix problems. In summary, the metagenomics CURE course was able to add to scientific knowledge and allowed students to participate in authentic research.

Microbially induced carbonate precipitation via methanogenesis pathway by a microbial consortium enriched from activated anaerobic sludge

AIMS

Various applications of microbially induced carbonate precipitation (MICP) has been proposed. However, most studies use cultured pure strains to obtain MICP, ignoring advantages of microbial consortia. The aims of this study were to: (i) test the feasibility of a microbial consortium to produce MICP; (ii) identify functional micro-organisms and their relationship; (iii) explain the MICP mechanism; (iv) propose a way of applying the MICP technique to soil media.

METHODS AND RESULTS

Anaerobic sludge was used as the source of the microbial consortium. A laboratory anaerobic sequencing batch reactor and beaker were used to perform precipitation experiment. The microbial consortium produced MICP with an efficiency of 96·6%. XRD and SEM analysis showed that the precipitation composed of different-size calcite crystals. According to high-throughput 16S rRNA gene sequencing, the functional micro-organisms included acetogenic bacteria, acetate-oxidizing bacteria and archaea Methanosaeta and Methanobacterium beijingense. The methanogenesis acetate degradation provides dissolved inorganic carbon and increases pH for MICP. A series of reactions catalysed by many enzymes and cofactors of methanogens and acetate-oxidizers are involved in the acetate degradation.

CONCLUSION

This work demonstrates the feasibility of using the microbial consortium to achieve MICP from an experimental and theoretical perspective.

SIGNIFICANCE AND IMPACT OF THE STUDY

A method of applying the microbial-consortium MICP to soil media is proposed. It has the advantages of low cost, low environmental impact, treatment uniformity and less limitations from natural soils. This method could be used to improve mechanical properties, plug pores and fix harmful elements of soil media, etc.

The biomethanation of cow manure in a continuous anaerobic digester can be boosted via a bioaugmentation culture containing Bathyarchaeota

A bioaugmentation approach was used to enhance the performance of anaerobic digestion (AD) using cow manure (CM) as the substrate in a continuous system. To obtain the desirable microbial culture for bioaugmentation, a biochemical methane potential test (BMP) was used to evaluate three commonly used inocula namely (1) municipal solid waste (MSW), (2) wastewater treatment plant (WWTP), and (3) cow manure digester (CMMD) for their hydrolytic capacity. The highest lignocellulose removal (56% for cellulose and 50% for hemicellulose) and the most profusion of cellulolytic bacteria were obtained when CM was inoculated with CMMD. CMMD was thus used as the seed inoculum in a continuously operated reactor (R_a) with the fiber fraction of CM as the substrate to further enrich cellulolytic microbes. After 100 days (HRT: 30 days), the Bacteria fraction mainly contained Ruminofilibacter, norank_o_SBR1031, Treponema, Acetivibrio. Surprisingly, the Archaea fraction contained 97% 'cellulolytic archaea' norank_c_Bathyarchaeia (Phylum Bathyarchaeota). This enriched consortium was used in the bioaugmentation experiment. A positive effect of bioaugmentation was verified, with a substantial daily methane yield (DMY) enhancement (24.3%) obtained in the bioaugmented reactor (R_b) (179 mL CH₄/gVS/d) than that of the control reactor (R_c) (144 mL CH₄/gVS/d) (P < 0.05). Meanwhile, the effluent of R_b enjoyed an improved cellulose reduction (14.7%) than that of R_c, whereas the amount of hemicellulose remained similar in both reactors' effluent. When bioaugmentation stopped, its influence on the hydrolysis and methanogenesis sustained, reflected by an improved DMY (160 mL CH₄/gVS/d) and lower cellulose content (53 mg/g TS) in R_b than those in R_c (DMY 144 mL/CH₄/gVS/d and cellulose content 63 mg/g TS, respectively). The increased DMY of the continuous reactor seeded with a specifically enriched consortium able to degrade the fiber fraction in CM shows the feasibility of applying bioaugmentation in AD of CM.

Aquipluma nitroreducens gen. nov. sp. nov., a novel facultatively anaerobic bacterium isolated from a freshwater lake

A novel facultatively anaerobic, nitrate-reducing bacterium, designated MeG22^T, was isolated from a freshwater lake in Japan. Cells of the strain were straight rods (0.8×2.5-10 µm), motile, and Gram-stain-negative. For growth, the optimum NaCl concentration was 0 % and the optimum temperature was 30 °C. Under anoxic conditions, strain MeG22^T reduced nitrate to nitrite. Major cellular fatty acids were C_15 : 1 ω6c (13.6 %), C_17 : 0 (11.9 %), anteiso-C_15 : 0 (10.6 %) and iso-C_15 : 0 (10.6 %). The major respiratory quinone was menaquinone-7. The genome sequence of strain MeG22^T consists of 5 712 279 bp with a G+C content of 40.3 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the family Prolixibacteraceae within the phylum Bacteroidetes. The closest relative of strain MeG22^T was Sunxiuqinia faeciviva strain JAM-BA0302^T with a 16S rRNA gene sequence similarity of 90.9 %. On the basis of phylogenetic and phenotypic characterization, Aquipluma nitroreducens, gen. nov., sp. nov., belonging to the family Prolixibacteraceae is proposed with the type strain MeG22^T (=NBRC 112896^T=DSM 106262^T).

Methanogenic pathway and microbial succession during start-up and stabilization of thermophilic food waste anaerobic digestion with biochar

One of the major obstacles for thermophilic anaerobic digestion is the process instability during start-up. This study proposed the use of a cost-effective additive, biochar, to accelerate and stabilize the start-up of thermophilic semi-continuous food waste anaerobic digestion. The results showed that the reactors with biochar addition resulted in up to 18% higher methane yield as compared to the control reactors (without biochar). The key microbial networks were elucidated through thermochemical and microbial analysis. Particularly, the addition of biochar promoted the growth of electroactive Clostridia and other electroactive bacteria, while the absence of biochar promoted the growth of homoacetogenic Clostridia and syntrophic acetate oxidizing bacteria. It was revealed that biochar promoted direct interspecies electron transfer between the microbes and was responsible for the faster degradation of volatile fatty acids. Furthermore, reactors with biochar also enhanced the thermodynamically favourable acetoclastic methanogenic pathway due to the higher abundance of Methanosarcina.

Tannins from senescent Rhizophora mangle mangrove leaves have a distinctive effect on prokaryotic and eukaryotic communities in a Distichlis spicata salt marsh soil

Due to climate warming, tannin-rich Rhizophora mangle migrates into tannin-poor salt marshes, where the tannins interfere with the biogeochemistry in the soil. Changes in biogeochemistry are likely associated with changes in microbial communities. This was studied in microcosms filled with salt marsh soil and amended with leaf powder, crude condensed tannins, purified condensed tannins (PCT), all from senescent R. mangle leaves, or with tannic acid. Size and composition of the microbial communities were determined by denaturing gradient gel electrophoresis, high-throughput sequencing and real-time PCR based on the 16S and 18S rRNA genes. Compared with the control, the 16S rRNA gene abundance was lowered by PCT, while the 18S rRNA gene abundance was enhanced by all treatments. The treatments also affected the composition of the 16S rRNA and 18S rRNA gene assemblies, but the effects on the 18S rRNA gene were greater. The composition of the 18S rRNA gene, but not of the 16S rRNA gene, was significantly correlated with the mineralization of carbon, nitrogen and phosphorus. Distinctive microbial groups emerged during the different treatments. This study revealed that migration of mangroves may affect both the prokaryotic and the eukaryotic communities in salt marsh soils, but that the effects on the eukaryotes will likely be greater.

Mangrovibacterium lignilyticum sp. nov., a facultatively anaerobic lignin-degrading bacterium isolated from mangrove sediment

An alkali lignin-degrading, Gram-stain-negative, rod-shaped, non-motile and facultatively anaerobic bacterium, designated BM_7^T, was isolated from mangrove sediment of the supralittoral zone in the Jiulong river estuary, PR China. The cells of strain BM_7^T were 0.4-0.6 µm wide and 1.0-8.5 µm long. Oxidase and catalase activities were positive. Strain BM_7^T could grow at 10-37 °C (optimum, 25-28 °C), at pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 0.5-6 % (w/v) NaCl (optimum, 2%). Phylogenetic analysis of 16S rRNA gene sequences indicated that strain BM_7^T belonged to the genus Mangrovibacterium of the family Prolixibacteraceae. It showed the highest similarity to Mangrovibacterium diazotrophicum JCM 19152^T (96.8 %), followed by Mangrovibacterium marinum KCTC 42253^T (96.1%). The values of average nucleotide identity and DNA-DNA hybridization were calculated as 76.9, 24.3 and 76.1, 17.4 % between strain BM_7^T with M. diazotrophicum JCM 19152^T and M. marinum KCTC 42253^T, respectively. The major respiratory quinone of strain BM_7^T was MK-7. The polar lipids were detected as phosphatidylethanolamine, three unidentified phospholipids and four unidentified aminolipids. The dominant fatty acids consisted of iso-C_15 : 0, anteiso-C_15 : 0, C_15 : 1  ω6c, iso-C_17 : 0 3-OH, C_17 : 1  ω6c, C_17 : 0 3-OH and C_17 : 0. The genome size of strain BM_7^T is 5.6 Mb, with G+C content of 43.4 mol%. Based on the phylogenetic and phenotypic characteristics, strain BM_7^T was considered to represent a novel species of the genus Mangrovibacterium, and the name Mangrovibacterium lignilyticum sp. nov. is proposed. The type strain is BM_7^T (=MCCC 1A15882^T=KCTC 72696^T).

Description of Maribellus sediminis sp. nov., a marine nitrogen-fixing bacterium isolated from sediment of cordgrass and mangrove

Two marine bacterial strains designated Y2-1-60^T and GM1-28 were isolated from sediments of cordgrass and mangrove along the Luoyang estuary in Quanzhou Bay, China, respectively. Both strains were Gram-staining-negative, straight rod-shaped, non-flagellum, facultatively anaerobic, nitrogen-fixing, and did not contain carotenoid pigment. Catalase activities were found to be weak positive and oxidase activities negative. The 16S rRNA gene sequences of the two strains were identical and had maximum similarity of 98.0% with Maribellus luteus XSD2^T, and of <94.5% with other species. ANI value (96.9%) and DDH estimate (71.5%) between the two strains supported that they belonged to the same species. ANI value and DDH estimate between the two strains and M. luteus XSD2^T was 74.3% and 19.4%, respectively, indicating that they represent a novel species. Phylogenetic analysis based on 16S rRNA gene and phylogenomic analysis indicated that strains Y2-1-60^T and GM1-28 formed a monophyletic branch within the genus Maribellus. The respiratory quinone was menaquinone MK-7. The major fatty acid (>10%) consisted of iso-C_15:0, and iso-C_17:0 3-OH. The polar lipids consisted of phosphatidylethanolamine and several unidentified lipids. The genomic G+C contents were 41.9-42.0mol%. Gene annotation revealed that strains Y2-1-60^T and GM1-28 contained a set of nif gene cluster (nifHDKENB) responsible for nitrogen fixation. Based on the above characteristics, strains Y2-1-60^T and GM1-28 represent a novel species within the genus Maribellus. Thus, Maribellus sediminis sp. nov. is proposed with type strain Y2-1-60^T (=MCCC 1K04285^T=KCTC 72884^T), isolated from cordgrass sediment and strain GM1-28 (=MCCC 1K04384=KCTC 72880), isolated from mangrove sediment.

Puteibacter caeruleilacunae gen. nov., sp. nov., a facultatively anaerobic bacterium isolated from Yongle Blue Hole in the South China Sea

Blue holes are unique geomorphological units characterized by steep redox and biogeochemical gradients. Yongle Blue Hole is located on the largest atoll (Yongle Atoll) of the western Xisha Islands in the South China Sea. A Gram-stain-negative, facultatively anaerobic, non-motile, non-flagellated marine bacterium with creamy white colonies, designated JC036T, was isolated from Yongle Blue Hole. Cells were short-rod-shaped and catalase-negative. 16S rRNA gene sequence analysis showed that sequence similarities were lower than 91.6 % against all validly named species in the familyProlixibacteraceae; a reconstructed phylogenetic tree indicated that strain JC036Tformed a lineage with strains in the familyProlixibacteraceae. Growth occurred at 4–37 °C (optimum, 28 °C), at pH 5.0–9.0 (optimum, 7.0) and in the presence of 2–6 % (w/v) NaCl (optimum, 3 %). The prevalent isoprenoid quinone of strain JC036Twas menaquinone-7 (MK-7). Iso-C15 : 0and iso-C17 : 03-OH were the predominant fatty acids. The major polar lipids included a phospholipid, phosphatidylethanolamine, an aminophospholipid and four unidentified lipids. The genomic DNA G+C content of strain JC036Twas 37.8 mol%. Based on physiological and biochemical characteristics and whole genome comparisons, we propose a new genus and species,Puteibacter caeruleilacunaegen. nov., sp. nov., within the familyProlixibacteraceae. The type strain ofPuteibacter caeruleilacunaeis JC036T(=JCM 33128T=MCCC 1K03579T). From this study, a deeper understanding of the community of the microorganism and their roles in biogeochemical cycles, especially anaerobic bacteria, is provided.

Characterizing phenol-removing consortia under methanogenic and sulfate-reducing conditions: potential metabolic pathways

Phenol removal was investigated in anaerobic fixed-structured bed reactors, namely R1 and R2, treating synthetic wastewater simulating the soluble fraction of vinasse under strictly methanogenic (R1) and simultaneous methanogenic/sulfidogenic conditions (R2). Next-generation sequencing (Illumina MiSeq System) was used to further characterize the microbial communities in both systems. Phenol was completely and stably removed in R1 after a short operating period (≈55 days). Conversely, phenol removal in R2 required a longer period for biomass acclimation (≈125 days) to reach levels equivalent to R1. Volatile fatty acids (VFA) accumulation in R2, mainly due to the inhibition of the acetoclastic methanogenesis by sulfide, may have limited phenol removal in the initial operating phases, as intermediate steps from phenol degradation are thermodynamically dependent on the removal of acetate, hydrogen and bicarbonate. Overall, the potential for anaerobically removing phenol from complex wastewaters was confirmed, even at low phenol/COD ratios. 16S rRNA gene sequencing analysis showed a high correlation of taxonomic profile between R1 and the inoculum, whereas a lower correlation was observed between R2 and the inoculum samples. Functional inference further indicated that Syntrophus and Bacillus genera in R1 and Clostridium genus in both reactors possibly played a key-role in phenol degradation.

Degradation of guar in an up-flow anaerobic sludge blanket reactor: Impacts of salinity on performance robustness, granulation and microbial community

Guar is extensively used during shale gas exploitation and is a major component in the flowback water. The viscosity of guar has adverse effects for the treatment of flowback water. This study investigated the degradation of guar at different salinities with an up-flow anaerobic sludge blanket (UASB) reactor. The effects of salinity on guar degradation, granular characteristics and microbial community were also studied. Results showed that more than 79% of guar was removed at hydraulic retention time (HRT) of 10 h, even at a concentration of 10000 mg L^-1 of NaCl. Increasing salinity decreased granular size and hydrophobicity, but improved the secretion of EPS (especially for protein). Low salt condition 2500 mg L^-1 presented faster degradation rate of guar. Salinity resulted in insignificant difference on bacterial community, but decreased the abundance of methanogens. Bacteroides, Prolixibacter and Pelolinea are essential genera in guar degradation. The results demonstrated the potential of UASB in the treatment of flowback water.

The Composition, Diversity and Predictive Metabolic Profiles of Bacteria Associated With the Gut Digesta of Five Sea Urchins in Luhuitou Fringing Reef (Northern South China Sea)

Sea urchins strongly affect reef ecology, and the bacteria associated with their gut digesta have not been well studied in coral reefs. In the current study, we analyze the bacterial composition of five sea urchin species collected from Luhuitou fringing reef, namely Stomopneustes variolaris, Diadema setosum, Echinothrix calamaris, Diadema savignyi, and Tripneustes gratilla, using high-throughput 16S rRNA gene-based pyrosequencing. Propionigenium, Prolixibacter, and Photobacterium were found to be the dominant bacterial genera in all five species. Interestingly, four sea urchin species, including S. variolaris, D. setosum, E. calamaris, and D. savignyi, displayed a higher mean total abundance of the three bacterial genera (69.72 ± 6.49%) than T. gratilla (43.37 ± 13.47%). Diversity analysis indicated that the gut digesta of sea urchin T. gratilla displayed a higher bacterial α-diversity compared with the other four species. PCoA showed that the four groups representing D. setosum, D. savignyi, E. calamaris, and S. variolaris were overlapping, but distant from the group representing T. gratilla. Predictive metagenomics performed by PICRUSt revealed that the abundances of genes involved in amino acid metabolism and metabolism of terpenoid and polyketide were higher in T. gratilla, while those involved in carbohydrate metabolism were higher in the other four sea urchin species. Therefore, our results indicated that the composition, diversity and predictive metabolic profiles of bacteria associated with the gut digesta of T. gratilla were significantly different from those of the other four sea urchin species in Luhuitou fringing reef.

As release under the microbial sulfate reduction during redox oscillations in the upper Mekong delta aquifers, Vietnam: A mechanistic study

The impact of seasonal fluctuations linked to monsoon and irrigation generates redox oscillations in the subsurface, influencing the release of arsenic (As) in aquifers. Here, the biogeochemical control on As mobility was investigated in batch experiments using redox cycling bioreactors and As- and SO₄^2--amended sediment. Redox potential (E_h) oscillations between anoxic (-300-0 mV) and oxic condition (0-500 mV) were implemented by automatically modulating an admixture of N₂/CO₂ or compressed air. A carbon source (cellobiose, a monomer of cellulose) was added at the beginning of each reducing cycle to stimulate the metabolism of the native microbial community. Results show that successive redox cycles can decrease arsenic mobility by up to 92% during reducing conditions. Anoxic conditions drive mainly the conversion of soluble As(V) to As(III) in contrast to oxic conditions. Phylogenetic analyses of 16S rRNA amplified from the sediments revealed the presence of sulfate and iron - reducing bacteria, confirming that sulfate and iron reduction are key factors for As immobilization from the aqueous phase. As and S K-edge X-ray absorption spectroscopy suggested the association of Fe-(oxyhydr)oxides and the importance of pyrite (FeS_2(s)), rather than poorly ordered mackinawite (FeS_(s)), for As sequestration under oxidizing and reducing conditions, respectively. Finally, these findings suggest a role for elemental sulfur in mediating aqueous thioarsenates formation in As-contaminated groundwater of the Mekong delta.

Microbial Community Composition and Putative Biogeochemical Functions in the Sediment and Water of Tropical Granite Quarry Lakes

Re-naturalized quarry lakes are important ecosystems, which support complex communities of flora and fauna. Microorganisms associated with sediment and water form the lowest trophic level in these ecosystems and drive biogeochemical cycles. A direct comparison of microbial taxa in water and sediment microbial communities is lacking, which limits our understanding of the dominant functions that are carried out by the water and sediment microbial communities in quarry lakes. In this study, using the 16S rDNA amplicon sequencing approach, we compared microbial communities in the water and sediment in two re-naturalized quarry lakes in Singapore and elucidated putative functions of the sediment and water microbial communities in driving major biogeochemical processes. The richness and diversity of microbial communities in sediments of the quarry lakes were higher than those in the water. The composition of the microbial communities in the sediments from the two quarries was highly similar to one another, while those in the water differed greatly. Although the microbial communities of the sediment and water samples shared some common members, a large number of microbial taxa (at the phylum and genus levels) were prevalent either in sediment or water alone. Our results provide valuable insights into the prevalent biogeochemical processes carried out by water and sediment microbial communities in tropical granite quarry lakes, highlighting distinct microbial processes in water and sediment that contribute to the natural purification of the resident water.

Co-occurrence network analysis reveals thermodynamics-driven microbial interactions in methanogenic bioreactors

Methanogenic bioreactors have been applied to treat purified terephthalic acid (PTA) wastewater containing complex aromatic compounds, such as terephthalic acid, para-toluic acid and benzoic acid. This study characterized the interaction of microbial populations in 42 samples obtained from 10 PTA-degrading methanogenic bioreactors. Approximately, 54 dominant populations (11 methanogens, 8 syntrophs and 35 functionally unknown clades) that represented 73.9% of total 16S rRNA gene iTag sequence reads were identified. Co-occurrence analysis based on the abundance of dominant OTUs showed two non-overlapping networks centred around aromatic compound- (group AR: Syntrophorhabdaceae, Syntrophus and Pelotomaculum) and fatty acid- (group FA: Smithella and Syntrophobacter) degrading syntrophs. Group AR syntrophs have no direct correlation with hydrogenotrophic methanogens, while those from group FA do. As degradation of aromatic compounds has a wider thermodynamic window than fatty acids, Group AR syntrophs may be less influenced by fluctuations in hydrogenotrophic methanogen abundance or may non-specifically interact with diverse methanogens. In both groups, network analysis reveals full-scale- and lab-scale-specific uncultivated taxa that may mediate interactions between syntrophs and methanogens, suggesting that those uncultivated taxa may support the degradation of aromatic compounds through uncharted ecophysiological traits. These observations suggest that organisms from multiple niches orchestrate their metabolic capacity in multiple interaction networks to effectively degrade PTA wastewater.

Enhancing Biochemical Methane Potential and Enrichment of Specific Electroactive Communities from Nixtamalization Wastewater using Granular Activated Carbon as a Conductive Material

Nejayote (corn step liquor) production in Mexico is approximately 1.4 × 1010 m3 per year and anaerobic digestion is an effective process to transform this waste into green energy. The biochemical methane potential (BMP) test is one of the most important tests for evaluating the biodegradability and methane production capacity of any organic waste. Previous research confirms that the addition of conductive materials significantly enhances the methane production yield. This study concludes that the addition of granular activated carbon (GAC) increases methane yield by 34% in the first instance. Furthermore, results show that methane production is increased by 54% when a GAC biofilm is developed 10 days before undertaking the BMP test. In addition, the electroactive population was 30% higher when attached to the GAC than in control reactors. Moreover, results show that electroactive communities attached to the GAC increased by 38% when a GAC biofilm is developed 10 days before undertaking the BMP test, additionally only in these reactors Geobacter was identified. GAC has two main effects in anaerobic digestion; it promotes direct interspecies electron transfer (DIET) by developing an electro-active biofilm and simultaneously it reduces redox potential from −223 mV to −470 mV. These results suggest that the addition of GAC to biodigesters, improves the anaerobic digestion performance in industrial processed food waste.

Microbial Community Changes in a Chlorinated Solvents Polluted Aquifer Over the Field Scale Treatment With Poly-3-Hydroxybutyrate as Amendment

This study investigated the organohalide-respiring bacteria (OHRB) and the supporting microbial populations operating in a pilot scale plant employing poly-3-hydroxybutyrate (PHB), a biodegradable polymer produced by bacteria from waste streams, for the in situ bioremediation of groundwater contaminated by chlorinated solvents. The bioremediation was performed in ground treatment units, including PHB reactors as slow release source of electron donors, where groundwater extracted from the wells flows through before the re-infiltration to the low permeability zones of the aquifer. The coupling of the biological treatment with groundwater recirculation allowed to drastically reducing the contamination level and the remediation time by efficiently stimulating the growth of autochthonous OHRB and enhancing the mobilization of the pollutants. Quantitative PCR performed along the external treatment unit showed that the PHB reactor may efficiently act as an external incubator to growing Dehalococcoides mccartyi, known to be capable of fully converting chlorinated ethenes to innocuous end-products. The slow release source of electron donors for the bioremediation process allowed the establishment of a stable population of D. mccartyi, mainly carrying bvcA and vcrA genes which are implicated in the metabolic conversion of vinyl chloride to harmless ethene. Next generation sequencing was performed to analyze the phylogenetic diversity of the groundwater microbiome before and after the bioremediation treatment and allowed the identification of the microorganisms working closely with organohalide-respiring bacteria.

Effects of coffee processing residues on anaerobic microorganisms and corresponding digestion performance

The objective of this study was to delineate the effects of different coffee processing residues on the anaerobic microbes and corresponding digestion performance. The results elucidated that mucilage-rich feed enhanced the accumulation of methanogens, which consequently led to better digestion performance of biogas production. Fifty percent more methane and up to 3 times more net energy (heat and electricity) output were achieved by the digestion of the mucilage-rich feed (M3). The microbial community and statistical analyses further elucidated that different residues in the feed had significant impact on microbial distribution and correspondingly influenced the digestion performance.

Effect of reclaimed water effluent on bacterial community structure in the Typha angustifolia L. rhizosphere soil of urbanized riverside wetland, China

In order to evaluate the impact of reclaimed water on the ecology of bacterial communities in the Typha angustifolia L. rhizosphere soil, bacterial community structure was investigated using a combination of terminal restriction fragment length polymorphism and 16S rRNA gene clone library. The results revealed significant spatial variation of bacterial communities along the river from upstream and downstream. For example, a higher relative abundance of γ-Proteobacteria, Firmicutes, Chloroflexi and a lower proportion of β-Proteobacteria and ε-Proteobacteria was detected at the downstream site compared to the upstream site. Additionally, with an increase of the reclaimed water interference intensity, the rhizosphere bacterial community showed a decrease in taxon richness, evenness and diversity. The relative abundance of bacteria closely related to the resistant of heavy-metal was markedly increased, while the bacteria related for carbon/nitrogen/phosphorus/sulfur cycling wasn't strikingly changed. Besides that, the pathogenic bacteria markedly increased in the downstream rhizosphere soil since reclaimed water supplement, while the possible plant growth-promoting rhizobacteria obviously reduced in the downstream sediment. Together these data suggest cause and effect between reclaimed water input into the wetland, shift in bacterial communities through habitat change, and alteration of capacity for biogeochemical cycling of contaminants.

Start-up and microbial communities of a simultaneous nitrogen removal system for high salinity and high nitrogen organic wastewater via heterotrophic nitrification

In this study, a simultaneous nitrogen removal system for high salinity and high nitrogen organic wastewater was developed in a pressurized biofilm reactor. The result showed that under the air supply rate of 200Lh(-1), salinity of 3.0±0.2%, organic load of 10kgCODm(-3)d(-1) and nitrogen loading of 0.185kgm(-3)d(-1), the reactor started up rapidly and performed stably after 30days operation. Meanwhile, a simultaneous COD and nitrogen removal was achieved in the single-stage reactor, with COD, NH4(+)-N and TN removal efficiency of 97%, 99% and 98%, respectively. Denaturing gradient gel electrophoresis profile demonstrated that simultaneous nitrogen removal could be achieved through heterotrophic nitrification-aerobic denitrification, and the pivotal microorganisms were Flavobacterium phragmitis and Paracoccus denitrificans. The microbial community of salt-tolerant halophilic microorganisms was developed successfully. This study can provide a more efficient and feasible solution to treat high salinity organic wastewater.

Surveys, simulation and single-cell assays relate function and phylogeny in a lake ecosystem

Much remains unknown about what drives microbial community structure and diversity. Highly structured environments might offer clues. For example, it may be possible to identify metabolically similar species as groups of organisms that correlate spatially with the geochemical processes they carry out. Here, we use a 16S ribosomal RNA gene survey in a lake that has chemical gradients across its depth to identify groups of spatially correlated but phylogenetically diverse organisms. Some groups had distributions across depth that aligned with the distributions of metabolic processes predicted by a biogeochemical model, suggesting that these groups performed biogeochemical functions. A single-cell genetic assay showed, however, that the groups associated with one biogeochemical process, sulfate reduction, contained only a few organisms that have the genes required to reduce sulfate. These results raise the possibility that some of these spatially correlated groups are consortia of phylogenetically diverse and metabolically different microbes that cooperate to carry out geochemical functions.

Description of Ancylomarina subtilis gen. nov., sp. nov., isolated from coastal sediment, proposal of Marinilabiliales ord. nov. and transfer of Marinilabiliaceae, Prolixibacteraceae and Marinifilaceae to the order Marinilabiliales

A Gram-stain-negative, facultatively anaerobic, moderately halophilic, filamentous, non-motile bacterium, designated FA102T, was isolated from marine sediment from the coast of Weihai, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FA102T formed a distinct evolutionary lineage within the family Marinifilaceae and its closest relative was Marinifilum fragile JCM 15579T (93.2 % sequence similarity). The DNA G+C content of the novel strain was 36.5 mol%. The predominant cellular fatty acids and respiratory quinone were iso-C15 : 0 and iso-C15 : 0 3-OH, and MK-7, respectively. On the basis of the phylogenetic, phenotypic and physiological data, strain FA102T represents a novel genus and species, for which the name Ancylomarina subtilis gen. nov., sp. nov. is proposed. The type strain of Ancylomarina subtilis is FA102T (=KCTC 42257T=DSM 28825T=CICC 10902T). Furthermore, a new order named Marinilabiliales is proposed to accommodate three families previously classified in the order Bacteroidales. Marinilabiliales ord. nov. encompasses the families Marinilabiliaceae, Prolixibacteraceae and Marinifilaceae.

Kinetics and microbial ecology of batch sulfidogenic bioreactors for co-treatment of municipal wastewater and acid mine drainage

The kinetics and microbial ecology in sulfidogenic bioreactors used in a novel two-stage process for co-treatment of acid mine drainage (AMD) and municipal wastewater (MWW) were investigated. Michaelis-Menten modeling of COD oxidation by sulfate reducing bacteria (SRB) (Vmax=0.33mgL(-1)min(-1), Km=4.3mgL(-1)) suggested that the Vmax can be reasonably achieved given the typical COD values in MWW and anticipated mixing with AMD. Non-competitive inhibition modeling (Ki=6.55mgL(-1)) indicated that excessive iron level should be avoided to limit its effects on SRB. The COD oxidation rate was positively correlated to COD/sulfate ratio and SRB population, as evidenced by dsrA gene copies. Phylogenetic analysis revealed diverse microbial communities dominated by sulfate reducing delta-proteobacteria. Microbial community and relative quantities of SRB showed significant differences under different COD/sulfate ratios (0.2, 1 and 2), and the highest dsrA gene concentration and most complex microbial diversity were observed under COD/sulfate ratio 2. Major species were associated with Desulfovirga, Desulfobulbus, Desulfovibrio, and Syntrophus sp. The reported COD kinetics, SRB abundances and the phylogenetic profile provide insights into the co-treatment process and help identify the parameters of concerns for such technology development.

Complete genome sequence of a deeply branched marine Bacteroidia bacterium Draconibacterium orientale type strain FH5(T)

Draconibacterium orientale strain FH5(T) isolated from a marine sediment sample from coast of Weihai, China, was a new species within the proposed new genus Draconibacterium in class Bacteroidia. Here, we present the genome sequence of D. orientale FH5(T), which contains 5,132,075 bp with a G+C content of 41.31%. The genome sequence will contribute to a better understanding of the physiology of this species.

Prolixibacter denitrificans sp. nov., an iron-corroding, facultatively aerobic, nitrate-reducing bacterium isolated from crude oil, and emended descriptions of the genus Prolixibacter and Prolixibacter bellariivorans

The facultatively aerobic, non-hydrogenotrophic, iron (Fe0)-corroding, nitrate-reducing Prolixibacter sp. strain MIC1-1T was characterized for representation of a novel species of the genus Prolixibacter. Strain MIC1-1T grew optimally at 35–37 °C, at pH 6.5 and with 2  % (w/v) NaCl. Strain MIC1-1T also grew fermentatively on some pentoses, hexoses, disaccharides and soluble starch. Succinic acid was the major end-product from d-glucose fermentation. Strain MIC1-1T was differentiated from the type strain of Prolixibacter bellariivorans by cell size, optimum growth temperature, range of temperature and NaCl for growth, and nitrate reduction. On the basis of phenotypic features and the phylogenetic position, a novel species of the genus Prolixibacter is proposed for strain MIC1-1T, to be named Prolixibacter denitrificans sp. nov. The type strain is MIC1-1T ( = JCM 18694T = NBRC 102688T = DSM 27267T). Emended descriptions of the genus Prolixibacter and Prolixibacter bellariivorans are also provided.

Roseimarinus sediminis gen. nov., sp. nov., a facultatively anaerobic bacterium isolated from coastal sediment

A Gram-stain-negative, facultatively anaerobic, non-motile and pink-pigmented bacterium, designated strain HF08T, was isolated from marine sediment of the coast of Weihai, China. Cells were rod-shaped, and oxidase- and catalase-positive. The isolate grew optimally at 33 °C, at pH 7.5–8.0 and with 2–3 % (w/v) NaCl. The dominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C14 : 0. Menaquinone 7 (MK-7) was the major respiratory quinone and the DNA G+C content was 44.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the class Bacteroidia, and shared 88–90 % sequence similarity with the closest genera Sunxiuqinia, Prolixibacter, Draconibacterium, Mariniphaga and Meniscus. Based on the phylogenetic and phenotypic evidence presented, a novel species in a new genus of the family Prolixibacteraceae is proposed, with the name Roseimarinus sediminis gen. nov., sp. nov. The type strain of Roseimarinus sediminis is HF08T ( = KCTC 42261T = CICC 10901T).

The impact of gamma radiation on sediment microbial processes

Microbial communities have the potential to control the biogeochemical fate of some radionuclides in contaminated land scenarios or in the vicinity of a geological repository for radioactive waste. However, there have been few studies of ionizing radiation effects on microbial communities in sediment systems. Here, acetate and lactate amended sediment microcosms irradiated with gamma radiation at 0.5 or 30 Gy h(-1) for 8 weeks all displayed NO3 (-) and Fe(III) reduction, although the rate of Fe(III) reduction was decreased in 30-Gy h(-1) treatments. These systems were dominated by fermentation processes. Pyrosequencing indicated that the 30-Gy h(-1) treatment resulted in a community dominated by two Clostridial species. In systems containing no added electron donor, irradiation at either dose rate did not restrict NO3 (-), Fe(III), or SO4 (2-) reduction. Rather, Fe(III) reduction was stimulated in the 0.5-Gy h(-1)-treated systems. In irradiated systems, there was a relative increase in the proportion of bacteria capable of Fe(III) reduction, with Geothrix fermentans and Geobacter sp. identified in the 0.5-Gy h(-1) and 30-Gy h(-1) treatments, respectively. These results indicate that biogeochemical processes will likely not be restricted by dose rates in such environments, and electron accepting processes may even be stimulated by radiation.

Draconibacterium filum sp. nov., a new species of the genus of Draconibacterium from sediment of the east coast of the Korean Peninsula

A Gram-stain negative, long rod shaped, facultatively anaerobic bacterium, designated strain F2(T), was isolated from coastal sediment of the Korean Peninsula. Strain F2(T) was found to grow at 10-40 °C (optimum 30 °C), at pH 6.0-8.5 (optimum pH 7.5) and at 0.0-8.0 % (w/v) NaCl (optimum 3.0 %). Phylogenetic analysis of the 16S rRNA gene sequence showed that strain F2(T) is closely related to Draconibacterium orientale FH5(T) (with 97.9 % 16S rRNA gene similarity) of the family Prolixibacteraceae of the phylum Bacteroidetes. The major isoprenoid quinone was identified as MK-7 and the main fatty acids as iso-C15:0 (24.1 %), anteiso-C15:0 (15.4 %), C16:0 (10.7 %), iso-C17:0 3-OH (7.6 %) and iso-C16:0 3-OH (5.9 %). The major polar lipids were identified as phosphatidylethanolamine, phosphatidylinositol and four unidentified polar lipids. The genomic DNA G+C content of strain F2(T) was determined to be 44.7 mol% and the DNA-DNA relatedness of strain F2(T) with D. orientale DSM 25947(T) was 34.6 ± 4.3 %. Nitrate reduction capability and cell morphology of strain F2(T) are distinct from those of the closest relative, D. orientale DSM 25947(T). Based on these properties, we propose strain F2(T) represents a novel species within the genus Draconibacterium, with the name Draconibacterium filum sp. nov. The type strain of D. filum is F2(T) (=KCTC 32486(T) = JCM 19986(T)).

Iron corrosion induced by nonhydrogenotrophic nitrate-reducing Prolixibacter sp. strain MIC1-1

Microbiologically influenced corrosion (MIC) of metallic materials imposes a heavy economic burden. The mechanism of MIC of metallic iron (Fe(0)) under anaerobic conditions is usually explained as the consumption of cathodic hydrogen by hydrogenotrophic microorganisms that accelerates anodic Fe(0) oxidation. In this study, we describe Fe(0) corrosion induced by a nonhydrogenotrophic nitrate-reducing bacterium called MIC1-1, which was isolated from a crude-oil sample collected at an oil well in Akita, Japan. This strain requires specific electron donor-acceptor combinations and an organic carbon source to grow. For example, the strain grew anaerobically on nitrate as a sole electron acceptor with pyruvate as a carbon source and Fe(0) as the sole electron donor. In addition, ferrous ion and l-cysteine served as electron donors, whereas molecular hydrogen did not. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MIC1-1 was a member of the genus Prolixibacter in the order Bacteroidales. Thus, Prolixibacter sp. strain MIC1-1 is the first Fe(0)-corroding representative belonging to the phylum Bacteroidetes. Under anaerobic conditions, Prolixibacter sp. MIC1-1 corroded Fe(0) concomitantly with nitrate reduction, and the amount of iron dissolved by the strain was six times higher than that in an aseptic control. Scanning electron microscopy analyses revealed that microscopic crystals of FePO4 developed on the surface of the Fe(0) foils, and a layer of FeCO3 covered the FePO4 crystals. We propose that cells of Prolixibacter sp. MIC1-1 accept electrons directly from Fe(0) to reduce nitrate.

Tangfeifania diversioriginum gen. nov., sp. nov., a representative of the family Draconibacteriaceae

A novel Gram-stain-negative, facultatively anaerobic, catalase- and oxidase-positive, non-motile and pink-pigmented bacterium, designated G22T, was isolated from Gahai, a saltwater lake in Qinghai province, China. Optimal growth occurred at 33–35 °C, pH 7.0–7.5, and in the presence of 2–4 % (w/v) NaCl. The DNA G+C content was 40.0 mol%. The major polar lipids were phosphatidylethanolamine and three unknown lipids. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH, and MK-7 was the main respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G22T fell within the class Bacteroidia . Its closest phylogenetic neighbour was the recently described species Draconibacterium orientale , the sole member of the family Draconibacteriaceae , with merely 90.04 % sequence similarity. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence observed, a novel species in a new genus, Tangfeifania diversioriginum gen. nov., sp. nov., is proposed within the family Draconibacteriaceae . The type strain is G22T ( = CICC 10587T = DSM 27063T).