Using Oxidative Electrodes to Enrich Novel Members in the Desulfobulbaceae Family from Intertidal Sediments

Members in the family of Desulfobulbaceae may be influential in various anaerobic microbial communities, including those in anoxic aquatic sediments and water columns, and within wastewater treatment facilities and bioelectrochemical systems (BESs) such as microbial fuel cells (MFCs). However, the diversity and roles of the Desulfobulbaceae in these communities have received little attention, and large portions of this family remain uncultured. Here we expand on findings from an earlier study (Li, Reimers, and Alleau, 2020) to more fully characterize Desulfobulbaceae that became prevalent in biofilms on oxidative electrodes of bioelectrochemical reactors. After incubations, DNA extraction, microbial community analyses, and microscopic examination, we found that a group of uncultured Desulfobulbaceae were greatly enriched on electrode surfaces. These Desulfobulbaceae appeared to form filaments with morphological features ascribed to cable bacteria, but the majority were taxonomically distinct from recognized cable bacteria genera. Thus, the present study provides new information about a group of Desulfobulbaceae that can exhibit filamentous morphologies and respire on the oxidative electrodes. While the phylogeny of cable bacteria is still being defined and updated, further enriching these members can contribute to the overall understanding of cable bacteria and may also lead to identification of successful isolation strategies.

Long-term biocide efficacy and its effect on a souring microbial community

Reservoir souring, which is the production of H 2 S mainly by sulfate-reducing microorganisms (SRM) in oil reservoirs, has been a long-standing issue for the oil industry. While biocides have been frequently applied to control biogenic souring, the effects of biocide treatment are usually temporary, and biocides eventually fail. The reasons behind biocide failure and the long-term response of the microbial community remain poorly understood. In this study, one time biocide treatments with glutaraldehyde (GA) and an aldehyde-releasing biocide (ARB) at low (100 ppm) and high (750 ppm) dosages were individually applied to a complex sulfate-reducing microbial community, followed by one-year monitoring of the chemical responses and the microbial community succession. The chemical results showed that souring control failed after 7 days at 100 ppm dosage regardless the biocide type, and that lasting souring control for the entire one-year timespan was only achieved with ARB at 750 ppm. Microbial community analyses suggested that the high dosage biocide treatments resulted in one order of magnitude lower average total microbial abundance and average SRM abundance compared to the low dosage treatments. The recurrence of souring was associated with reduction of alpha diversity and with long-term microbial community structure change, thus monitoring changes in microbial community metrics may serve as early warnings of the failure of a biocide-based souring control programme in the field. Furthermore, spore-forming sulfate reducers ( Desulfotomaculum and Desulfurispora ) were enriched and became dominant in both GA-treated groups, which could cause challenges to the design of long-lasting remedial souring control strategies. IMPORTANCE Reservoir souring is a detrimental problem for the oil and gas industry as H 2 S corrodes the steel infrastructure, downgrades the oil quality and poses substantial risks to the field personnel and the environment. Biocides have been widely applied to remedy souring, yet the long-term performance of biocide treatments is hard to predict or optimise due to limited understanding of the microbial ecology affected by biocide treatment. This study investigates the long-term biocide performance and associated changes in the abundance, diversity and structure of the souring microbial community, thus advancing the knowledge towards a deeper understanding of the microbial ecology of biocide-treated systems, and contributing to the improvement of current biocide-based souring control practices. The study showcases the potential application of incorporating microbial community analyses to forecast souring and highlights the long-term consequences of the biocide treatment on the microbial communities, with relevance to both operators and regulators.

Comparative Microbiome and Metabolome Analyses of the Marine Tunicate Ciona intestinalis from Native and Invaded Habitats

Massive fouling by the invasive ascidian Ciona intestinalis in Prince Edward Island (PEI, Canada) has been causing devastating losses to the local blue mussel farms. In order to gain first insights into so far unexplored factors that may contribute to the invasiveness of C. intestinalis in PEI, we undertook comparative microbiome and metabolome studies on specific tissues from C. intestinalis populations collected in invaded (PEI) and native regions (Helgoland and Kiel, Germany). Microbial community analyses and untargeted metabolomics revealed clear location- and tissue-specific patterns showing that biogeography and the sampled tissue shape the microbiome and metabolome of C. intestinalis. Moreover, we observed higher microbial and chemical diversity in C. intestinalis from PEI than in the native populations. Bacterial OTUs specific to C. intestinalis from PEI included Cyanobacteria (e.g., Leptolyngbya sp.) and Rhodobacteraceae (e.g., Roseobacter sp.), while populations from native sampling sites showed higher abundances of e.g., Firmicutes (Helgoland) and Epsilonproteobacteria (Kiel). Altogether 121 abundant metabolites were putatively annotated in the global ascidian metabolome, of which 18 were only detected in the invasive PEI population (e.g., polyketides and terpenoids), while six (e.g., sphingolipids) or none were exclusive to the native specimens from Helgoland and Kiel, respectively. Some identified bacteria and metabolites reportedly possess bioactive properties (e.g., antifouling and antibiotic) that may contribute to the overall fitness of C. intestinalis. Hence, this first study provides a basis for future studies on factors underlying the global invasiveness of Ciona species.

Arsenic mobilization by anaerobic iron-dependent methane oxidation

Arsenic groundwater contamination threatens the health of millions of people worldwide, particularly in South and Southeast Asia. In most cases, the release of arsenic from sediment was caused by microbial reductive dissolution of arsenic-bearing iron(III) minerals with organic carbon being used as microbial electron donor. Although in many arsenic-contaminated aquifers high concentrations of methane were observed, its role in arsenic mobilization is unknown. Here, using microcosms experiments and hydrogeochemical and microbial community analyses, we demonstrate that methane functions as electron donor for methanotrophs, triggering the reductive dissolution of arsenic-bearing iron(III) minerals, increasing the abundance of genes related to methane oxidation, and ultimately mobilizing arsenic into the water. Our findings provide evidence for a methane-mediated mechanism for arsenic mobilization that is distinct from previously described pathways. Taking this together with the common presence of methane in arsenic-contaminated aquifers, we suggest that this methane-driven arsenic mobilization may contribute to arsenic contamination of groundwater on a global scale.

Metagenome analyses reveal the role of Clostridium perfringens in alfalfa silage anaerobic deterioration

ABSTRACT The clostridial fermentation caused by the outgrowth of Clostridia was mainly responsible for the silage anaerobic deterioration. Our previous results showed that Clostridium perfringens dominated the clostridial community in poor-fermented alfalfa silage. This study was conducted to further examine the role of C. perfringens in silage anaerobic deterioration through fermentation products and the microbial community analyses. Direct-cut alfalfa was ensiled with C. perfringens contamination (CKC) or with the addition of Lactobacillus plantarum, sucrose and C. perfringens (LSC). Contamination with C. perfringens enhanced the clostridial fermentation in CKC silage, as indicated by high contents of butyric acid, ammonia nitrogen and Clostridia, while LSC silage was well preserved. The genera Bifidobacterium, Garciella and Clostridium dominated the bacterial community in CKC silage, while predominate genus was replaced by Lactobacillus in LSC silage. The clostridial community in CKC silage was dominated by Garciella sp. (26.9 to 58.1%) and C. tyrobutyricum (24.4 to 48.6%), while the relative abundance of C. perfringens was below 5.0%. Therefore, the effect of Clostridia contamination on ensiling fermentation was dependent on the ensilability of the silage material. Garciella sp. and C. tyrobutyricum, rather than C. perfringens, played dominant role in the clostridial fermentation in CKC silage.