Clostridium aquiflavi sp. nov., isolated from yellow water of Nongxiangxing baijiu in the Yibin region of China

A Gram-stain-positive, strictly anaerobic, endospore-forming and rod-shaped (0.6-0.8×2.7-13.1 µm) bacterium, designated as 5 N-1T, was isolated from a yellow water sample collected from the manufacturing process of Nongxiangxing baijiu in the Yibin region of Sichuan, PR China. Growth occurred at 15-40 °C (optimum growth at 37 °C), at pH 6.0-9.0 (optimum growth at pH 7.0) and in NaCl concentrations of 0-1 % (w/v) and ethanol concentrations of 0-2 % (v/v). The major fatty acids in strain 5 N-1T were C16 : 0, C18 : 0 and C14 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified aminophospholipids and one unidentified lipid. Phylogenetic analysis of its 16S rRNA gene sequence indicated that strain 5 N-1T was most closely related to Clostridium weizhouense YB-6T (97.70 %) and Clostridium uliginosum DSM 12992T (97.56 %). The average nucleotide identity and digital DNA‒DNA hybridization values between strain 5 N-1T and the above two type strains were 80.89 and 80.05 % and 25.80 and 25.30 %, respectively, which were all below the species thresholds. The genome size of strain 5 N-1T was 3.5 Mbp and the DNA G+C content was 27.5 mol%. Based on the results of phenotypic and genotypic analyses, strain 5 N-1T represents a novel species of the genus Clostridium, for which the name Clostridium aquiflavi sp. nov. is proposed. The type strain is Clostridium aquiflavi 5 N-1T (=CICC 24886T=JCM 35355T).

Planktonic and epilithic prokaryota community compositions in a large temperate river reflect climate change related seasonal shifts

In freshwaters, microbial communities are of outstanding importance both from ecological and public health perspectives, however, they are threatened by the impact of global warming. To reveal how different prokaryotic communities in a large temperate river respond to environment conditions related to climate change, the present study provides the first detailed insight into the composition and spatial and year-round temporal variations of planktonic and epilithic prokaryotic community. Microbial diversity was studied using high-throughput next generation amplicon sequencing. Sampling was carried out monthly in the midstream and the littoral zone of the Danube, upstream and downstream from a large urban area. Result demonstrated that river habitats predominantly determine the taxonomic composition of the microbiota; diverse and well-differentiated microbial communities developed in water and epilithon, with higher variance in the latter. The composition of bacterioplankton clearly followed the prolongation of the summer resulting from climate change, while the epilithon community was less responsive. Rising water temperatures was associated with increased abundances of many taxa (such as phylum Actinobacteria, class Gammaproteobacteria and orders Synechococcales, Alteromonadales, Chitinophagales, Pseudomonadales, Rhizobiales and Xanthomonadales), and the composition of the microbiota also reflected changes of several further environmental factors (such as turbidity, TOC, electric conductivity, pH and the concentration of phosphate, sulphate, nitrate, total nitrogen and the dissolved oxygen). The results indicate that shift in microbial community responding to changing environment may be of crucial importance in the decomposition of organic compounds (including pollutants and xenobiotics), the transformation and accumulation of heavy metals and the occurrence of pathogens or antimicrobial resistant organisms.

Effect of Multiple Rounds of Enrichment on Metabolite Accumulation and Microbiota Composition of Pit Mud for Baijiu Fermentation

Pit mud (PM) is the main component of Baijiu (traditional Chinese liquor), and its microorganisms are the primary sources of the aroma of Chinese strong-flavor Baijiu (SFB). Enrichment plays an important role in the selection of functional microorganisms in PM. Herein, the PM of SFB was submitted to six rounds of enrichment using clostridial growth medium (CGM), and changes in the metabolite accumulation and microbiota composition were evaluated. Based on the metabolite production and microbiota composition, the enrichment rounds were classified as the acclimation stage (round 2), main fermentation stage (rounds 3 and 4), and late fermentation stage (rounds 5 and 6). Species within the genus Clostridium dominated in the acclimation stage (65.84-74.51%). In the main fermentation stage, the dominant microbial groups were producers of butyric acid, acetic acid, and caproic acid, which included Clostridium (45.99-74.80%), Caproicibacter (1.45-17.02%), and potential new species within the order of Oscillataceae (14.26-29.10%). In the late stage of enrichment, Pediococcus dominated (45.96-79.44%). Thus, the main fermentation stage can be considered optimal for the isolation of acid-producing bacteria from PM. The findings discussed herein support the development and application of functional bacteria by bioaugmentation, and contribute to improving the quality of PM and SFB production.

Clostridium btbubcensis BJN0001, a potentially new species isolated from the cellar mud of Chinese strong-flavor baijiu, produces ethanol, acetic acid and butyric acid from glucose

A novel strain, designated BJN0001, was isolated from the cellar mud of Chinese strong-flavor baijiu. The complete genome of strain BJN0001 was 2,688,791 bp and annotated with 2610 genes. Whole-genome similarity metrics such as average nucleotide identity (ANI) of BJN0001 with reference genomes reveals clear species boundaries of < 95% ANI value for species. The DNA-DNA hybridization (DDH) values of BJN0001 with the type species were all lower than 70% DDH value for species. Based on these results, the strain BJN0001 was considered a potentially new species of the genus Clostridium. Meanwhile, the fermentation characteristics indicated that the strain had the capability to convert glucose to ethanol, acetic acid and butyric acid, which could provide basic data for revealing its function in baijiu fermentation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03271-7.

Clostridium gelidum sp. nov., a psychrotrophic anaerobic bacterium isolated from rice field soil

A cold-adapted or psychrotrophic anaerobic bacterial strain (C5S11T) was isolated from rice field soil in Japan using an enrichment culture incubated at 5 °C. C5S11T grew at 0 °C and optimum growth was observed at 10 °C. Cells of C5S11T were Gram-stain-positive, motile, spore-forming rods with peritrichous flagella. C5S11T was assigned to a large branch consisted of various mesophilic species of the genus Clostridium in the phylogenetic trees reconstructed using the 16S rRNA gene sequences. The most closely related species of the strain was Clostridium chromiireducens DSM 23318T (98.5 % sequence similarity). C5S11T fermented various carbohydrates, including polysaccharides (starch, inulin, pectin and xylan), and produced acetate, butyrate and H2 as major products. The major cellular fatty acids were C16 : 0, C16 : 1ω9c, C14 : 0 and C16 : 1ω7c. The diagnostic diamino acid of the cell wall peptidoglycan was meso-diaminopimelic acid. The genome size of C5S11T was 6.04 Mb and the genomic DNA G+C content was 29.0 mol%. Average nucleotide identity by blast (ANIb), avaerage amino acid identity (AAI) and digital DNA–DNA hybridization (dDDH) values between the genomes of C5S11T and C. chromiireducens DSM 23318T were 80.0, 75.2 and 26.4 %, respectively. C5S11T had a gene encoding cold shock protein (RNA chaperone) in the genome, homologues of which have been found in psychrophilic species of the genus Clostridium . On the basis of the differences in the phylogenetic, genomic and phenotypic characteristics of C5S11T from those of the closely related species, a novel species, Clostridium gelidum sp. nov., is proposed to accommodate the strain. The type strain is C5S11T (=NBRC 114689T = DSM 112608T).

Potential for Natural Attenuation of Domestic and Agricultural Pollution in Karst Groundwater Environments

In karst areas, anthropogenic contaminants reach the subsurface with detrimental effects on the groundwater ecosystem and downstream springs, which often serve as drinking water sources for the local human communities. We analyzed the water chemistry and microbial community composition in upstream and downstream locations of five hydrokarst systems (HKS) during four seasons. Conductivity and nitrates were higher in the downstream springs than in the pre-karst waters, whereas the concentration of organic matter, considered here as a pollution indicator, was lower. The microbial community composition varied largely between upstream and downstream locations, with multiple species of potentially pathogenic bacteria decreasing in the HKS. Bacteria indicative of pollution decreased as well when passing through the HKS, but potential biodegraders increased. This suggests that the HKS can filter out part of the polluting organic matter and, with it, part of the associated microorganisms. Nevertheless, the water quality, including the presence of pathogens in downstream springs, must be further monitored to control whether the water is appropriate for consumption. In parallel, the human populations located upstream must be advised of the risks resulting from their daily activities, improper stocking of their various wastes and dumping of their refuse in surface streams.

Description of two novel anaerobic members in the family Clostridiaceae, Anaeromonas gelatinilytica gen.nov., sp. nov., and Anaeromonas frigoriresistens sp. nov., isolated from saline lake sediment

Cells of members of the family Clostridiaceae , phylum Firmicutes , are generally obligate anaerobic rods. Strains D2Q-14T and D2Q-11T were isolated from sediment of the saline lake Manisi in the Xinjiang Uygur Autonomous Region, PR China. In this study, we employed a polyphasic approach and whole genome analysis of the two isolates. Cells of both isolates were Gram-stain-positive rods that were motile by means of flagella and could utilize sulphate, thiosulphate, elemental sulphur and nitrate as electron acceptors. Phylogenetic analyses based on 16S rRNA gene and whole genome sequences indicated that strains D2Q-14T and D2Q-11T constituted a coherent cluster affiliated to the family Clostridiaceae . In addition, genome analysis revealed that strain D2Q-14Tharboured one nonribosomal peptide synthetase gene cluster, making up 1.4 % of the entire genome. The genome-based analysis, including average nucleotide identity, average amino acid identity and in silico DNA–DNA hybridization, biochemical, phenotypic and chemotaxonomic characterization, indicated that strains D2Q-14T and D2Q-11T represented two novel species of a novel genus in the family Clostridiaceae , for which we propose the names Anaeromonas gelatinilytica gen. nov., sp. nov. and Anaeromonas frigoriresistens sp. nov., with the type strains D2Q-14T (=KCTC 15986T=MCCC 1K04634T) and D2Q-11T (=KCTC 15985T=MCCC 1K04391T), respectively.

Clostridium weizhouense sp. nov., an anaerobic bacterium isolated from activated sludge of petroleum wastewater

A Gram-stain-positive, anaerobic, spore-forming, rod-shaped (0.4–0.6 µm×2.5–3.2 µm), flagellated bacterium, designated strain YB-6T, was isolated from activated sludge of an anaerobic tank at Weizhou marine oil mining wastewater treatment plant in Beihai, Guangxi, PR China. The culture conditions were 25–45 °C (optimum, 37 °C), pH 4–12 (pH 7.0) and NaCl concentration of 0–7 % w/v (0%). Strain YB-6T grew slowly in petroleum wastewater and removed 68.2 % of the total organic carbon in petroleum wastewater within 10 days. Concentrations of naphthalene, anthracene and phenanthrene at an initial concentration of 50 mg l−1 were reduced by 32.8, 40.4 and 14.6 %, respectively, after 7 days. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain YB-6T belongs to Clostridium cluster I and is most closely related to Clostridium uliginosum CK55T (98.5 % similarity). The genome size of strain YB-6T was 3.96 Mb, and the G+C content was 26.5 mol%. The average nucleotide identity value between strain YB-6T and C. uliginosum CK55T was 81.9 %. The major fatty acids in strain YB-6T were C14 : 0 FAME, C16 : 0 FAME and summed feature 4 (unknown 14.762 and/or C15 : 2 FAME). The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified aminophospholipids, one unidentified glycolipid and one unidentified aminolipid. Diaminopimelic acid was not detected in the strain YB-6T cell walls. Whole-cell sugars mainly consisted of ribose and galactose. Based on the results of phenotypic and genotypic analyses, strain YB-6T represents a novel species of the genus Clostridium , for which the name Clostridium weizhouense sp. nov. is proposed. The type strain is YB-6T (=GDMCC 1.2529T=JCM 34754T).

Aquaculture drives distinct patterns of planktonic and sedimentary bacterial communities: insights into co-occurrence pattern and assembly processes

Aquaculture would change the environmental condition in the lake ecosystem, affecting the structure and function of the aquatic ecosystem. However, little is known about the underlying mechanisms controlling the distribution patterns of bacterial community respond to aquaculture in water column and sediment. Here, we investigated the composition, co-occurrence patterns, and assembly processes of planktonic and sedimentary bacterial communities (PBC vs. SBC) from an aquaculture-influenced zone of the Eastern Lake Taihu, China. We found that aquaculture activity greatly influenced the diversity and composition of SBC by inducing excess nitrogen into the sediments. Meanwhile, network analysis revealed that aquaculture activity strengthened species interactions within the SBC network but weakened the species interactions within the PBC network. Aquaculture activity also increased the importance of deterministic processes governing the assembly of SBC by heightening the importance of environmental filtering, whereas it decreased the relative importance of deterministic processes within the assembly of PBC. In addition, ecological restoration with macrophytes increased the diversity of PBC and formed a more stable PBC network by increasing the number of network keystones. Overall, our results indicated that aquaculture drove distinct co-occurrence patterns and assembly mechanisms of PBC and SBC. This study has fundamental implications in the lake ecosystem for evaluating the microbially mediated ecological consequences of aquaculture.

Controlling pathogenic risks of water treatment biotechnologies at the source by genetic editing means

Antimicrobial-resistant pathogens in the environment and wastewater treatment systems, many of which are also important pollutant degraders and are difficult to control by traditional disinfection approaches, have become an unprecedented treat to ecological security and human health. Here, we propose the adoption of genetic editing techniques as a highly targeted, efficient and simple tool to control the risks of environmental pathogens at the source. An 'all-in-one' plasmid system was constructed in Aeromonas hydrophila to accurately identify and selectively inactivate multiple key virulence factor genes and antibiotic resistance genes via base editing, enabling significantly suppressed bacterial virulence and resistance without impairing their normal phenotype and pollutant-degradation functions. Its safe application for bioaugmented treatment of synthetic textile wastewater was also demonstrated. This genetic-editing technique may offer a promising solution to control the health risks of environmental microorganisms via targeted gene inactivation, thereby facilitating safer application of water treatment biotechnologies.

Adaptability of a caproate-producing bacterium contributes to its dominance in an anaerobic fermentation system

The transformation of diverse feedstocks into medium-chain fatty acids (MCFAs) by mixed cultures is a promising biorefinery route because of the high value of MCFAs. A particular concern is how to maintain the microbial consortia in mixed cultures to achieve stable MCFA production. Chinese strong aroma-type liquor (Baijiu) fermentation system continually produces caproic acid for decades through a spontaneous inoculation of anaerobes from pit mud into fermented grains. Therefore, illuminating the dominant caproate-producing bacterium (CPB) in pit mud and how the CPB sustains in the spontaneous fermentation system will benefit to reveal the microbiological mechanisms of the stable caproate production. Here, we examined pit mud samples across four Chinese strong aroma-type Baijiu producing areas and found that a caproate-producing Caproicibacterium sp. was widely distributed in these distilleries with relative abundance ranging from 1.4% to 35.5% and an average abundance of 11.4%. Through controlling carbon source availability, we achieved different simplified caproate-producing consortia and found that the growth advantage of Caproicibacterium sp. was highly dependent on glucose. Then two strains, named Caproicibacterium sp. LBM19010 and Caproicibacterium sp. JNU-WLY1368, were isolated from pit mud of two regions. The metabolic versatility of this bacterium utilizing starch, maltose, glucose and lactate reflected its adaptability to the fermentation environment where these carbon sources coexist. The simultaneous utilization of glucose and lactate contributed to the balance between cell growth and pH homeostasis. This study reveals that multiple adaptation strategies employed by the predominant CPB promotes its stability and dominance in a saccharide- and lactate-rich anaerobic habitat. IMPORTANCE Chinese strong aroma-type liquor (Baijiu) fermentation environment is a typical medium-chain fatty acid producing system with complex nutrients. Although several studies have revealed the correlation between microbial community composition and abiotic factors, the adaptation mechanisms of dominant species to abiotic environment are still unknown in this special anaerobic habitat. This study identified the predominant CPB in Chinese strong aroma-type Baijiu fermentation system. Metabolic versatility and flexibility of the dominant CPB with a small-size genome indicated that this bacterium can effectively exploit available carbon and nitrogen sources, which could be a key factor to promote its ecological success in a multi-species environment. The understanding of growth and metabolic features of CPB responsible for its dominance in microbial community will not only contribute to the improvement of Chinese strong aroma-type Baijiu production but also expand its potential industrial applications in caproate production.

Performance and mechanisms for V(v) bio-reduction by straw: key influencing factors

A high concentration of vanadium [V(v)] in groundwater is extremely harmful for humans. Weak movability and low toxicity after microbial V(v) reduction have attracted remarkable attention, especially for using solid carbon sources. However, the influencing factors remain unclear. In this study, the initial V(v) concentration, inocula amount and straw dosage were examined to ascertain the mechanisms behind them. Increasing the initial V(v) concentration led to the decrease of the V(v) removal efficiency, which was also positively correlated with the straw dosage within a certain range. The initial sludge amount was not a main factor affecting microbial V(v) removal in this study. With the initial amount of 10 mg L-1 V(v), 25 mL initial inocula and 5 g straw, 88.2% of V(v) was removed. According to the dissolved organic matter (DOM) analysis results, microbial activity prevailed in groups with higher V(v) removal efficiency, indicating that the V(v) bio-reduction was attributed to the microbial activity, which was considered a major factor. Functional species as unclassified_f_Enterobacteriaceae presumably contributed to the V(v) bioreduction, with upregulated ABC transporter genes and enzymes.

Enrichment of microbial communities for hexavalent chromium removal using a biofilm reactor

Given the toxicity and widespread occurrence of hexavalent chromium [Cr(VI)] in aquatic environments, we investigated the feasibility of a down-flow hanging sponge (DHS) biofilm reactor for the enrichment of microbial communities capable of Cr(VI) removal. In the present study, a laboratory-scale DHS reactor fed with a molasses-based medium containing Cr(VI) was operated for 112 days for the investigation. The enrichment of Cr(VI)-removing microbial communities was evaluated based on water quality and prokaryotic community analyses. Once the DHS reactor began to operate, high average volumetric Cr(VI) removal rates of 1.21-1.45 mg L-sponge^-1 h^-1 were confirmed under varying influent Cr(VI) concentrations (approximately 20-40 mg L^-1). 16S rRNA gene amplicon sequencing analysis suggested the presence of phylogenetically diverse prokaryotic lineages, including phyla that contain well-known Cr(VI)-reducing bacteria (e.g., Bacteroidetes, Firmicutes, and Proteobacteria) in the polyurethane sponge media of the DHS reactor. Therefore, our findings indicate that DHS reactors have great potential for the enrichment of Cr(VI)-removing microbial communities.

Isolation of Clostridium from Yunnan-Tibet hot springs and description of Clostridium thermarum sp. nov. with lignocellulosic ethanol production

Lignocellulose is considered a major source of renewable energy that serve as an alternative to the fossil fuels. Members of the genus Clostridium are some of the many microorganisms that have the ability to degrade lignocellulose efficiently to sugar, which can be further converted to biofuel. In this study, we isolated twelve Clostridium strains from hot spring samples of Yunnan and Tibet, of which isolates SYSU GA15002^T and SYSU GA17076 showed low 16S rRNA gene sequence identity profiles to any of the validly named Clostridium strains (<94.0%). Studies using a polyphasic taxonomy approach concluded that the two isolates represent one novel species of the genus Clostridium, for which we propose the name Clostridium thermarum sp. nov., with SYSU GA15002^T as the type strain of the species. Isolate SYSU GA15002^T has an optimum growth temperature at 45°C. Fermentation of the substrates cellobiose, cellulose, xylan and untreated straw powder by this strain results in the production of ethanol, along with acetate and formate. The complete pathways for the conversion of cellulose and xylan to ethanol is also predicted from the genome of isolate SYSU GA15002^T, which revealed a single step conversion of lignocellulosic biomass through consolidated bioprocessing. This paper is a comprehensive study encompassing isolation, polyphasic taxonomy, lignocellulose biodegradation and the genomic information of Clostridium in Yunnan-Tibet hot springs.

β-1,3-Glucanase production as an anti-fungal enzyme by phylogenetically different strains of the genus Clostridium isolated from anoxic soil that underwent biological disinfestation

Biological (or reductive) soil disinfestation (BSD or RSD) is a bioremediation process to control soil-borne plant pathogens using activities of indigenous bacteria in the soil. Three obligate anaerobic bacterial strains (TW1, TW10, and TB10), which were isolated from anoxic soil subjected to BSD treatments, were examined for their abilities to produce anti-fungal enzymes. All strains were affiliated with the different lineages of the genus Clostridium. The three strains decomposed β-1,3-glucans (curdlan and laminarin), and β-1,3-glucanase activities were detected from their culture supernatants with these glucans. The three strains also produced the enzyme with wheat bran as a growth substrate and killed the Fusarium pathogen (Fusarium oxysporum f. sp. spinaciae) in the anaerobic co-incubation conditions. Observation by fluorescence microscopy of the pathogen cells showed that the three strains had degraded the fungal cells in different manners upon co-incubation with wheat bran. When the three strains were cultivated with the dead cells or the cell wall samples prepared from the Fusarium pathogen, strain TW1 utilized these materials as easily decomposable substrates by releasing β-1,3-glucanase. When observed by fluorescence microscopy, it appeared that strain TW1 degraded the mycelial cell wall nearly thoroughly, with the septa remaining as undecomposed luminous rings. In contrast, the other two strains decomposed neither the dead cells nor the cell wall samples directly. The results indicate that the various anaerobic bacteria proliferated in the soil under the BSD treatments should play key roles as an organized bacterial community to eliminate fungal pathogens, namely by release of anti-fungal enzymes with different properties.

Key points •Three clostridial strains isolated from BSD-treated soils produced β-1,3-glucanase. •All strains killed the Fusarium pathogen in the anaerobic co-incubation conditions. •One of the strains produced β-1,3-glucanase with the fungal cell wall as a substrate. •The strain degraded the cell wall almost completely, except for the mycelial septa.

Microbial Assisted Hexavalent Chromium Removal in Bioelectrochemical Systems

Groundwater is the environmental matrix that is most frequently affected by anthropogenic hexavalent chromium contamination. Due to its carcinogenicity, Cr(VI) has to be removed, using environmental-friendly and economically sustainable remediation technologies. BioElectrochemical Systems (BESs), applied to bioremediation, thereby offering a promising alternative to traditional bioremediation techniques, without affecting the natural groundwater conditions. Some bacterial families are capable of oxidizing and/or reducing a solid electrode obtaining an energetic advantage for their own growth. In the present study, we assessed the possibility of stimulating bioelectrochemical reduction of Cr(VI) in a dual-chamber polarized system using an electrode as the sole energy source. To develop an electroactive microbial community three electrodes were, at first, inserted into the anodic compartment of a dual-chamber microbial fuel cell, and inoculated with sludge from an anaerobic digester. After a period of acclimation, one electrode was transferred into a polarized system and it was fixed at −0.3 V (versus standard hydrogen electrode, SHE), to promote the reduction of 1000 µg Cr(VI) L−1. A second electrode, served for the set-up of an open circuit control, operated in parallel. Cr(VI) dissolved concentration was analysed at the initial, during the experiment and final time by spectrophotometric method. Initial and final microbial characterization of the communities enriched in polarized system and open circuit control was performed by 16S rRNA gene sequencing. The bioelectrode set at −0.3 V showed high Cr(VI) removal efficiency (up to 93%) and about 150 µg L−1 day−1 removal rate. Similar efficiency was observed in the open circuit (OC) even at about half rate. Whereas, purely electrochemical reduction, limited to 35%, due to neutral operating conditions. These results suggest that bioelectrochemical Cr(VI) removal by polarized electrode offers a promising new and sustainable approach to the treatment of groundwater Cr(VI) plumes, deserving further research.

Flooding-Associated Soft Rot of Sweetpotato Storage Roots Caused by Distinct Clostridium Isolates

Flooding of sweetpotatoes in the field leads to development of soft rot on the storage roots while they remain submerged or on subsequent harvest and storage. Incidences of flooding after periods of intense rainy weather are on the rise in the southeastern United States, which is home to the majority of sweetpotato production in the nation. In an effort to characterize the causative agent(s) of this devastating disease, here we describe two distinct bacterial strains isolated from soft-rotted sweetpotato storage roots retrieved from an intentionally flooded field. Both of these anaerobic spore-forming isolates were identified as members of the genus Clostridium based on sequence similarity of multiple housekeeping genes, and both were confirmed to cause soft rot disease on sweetpotato and other vegetable crops. Despite these common features, the isolates were distinguishable by several phenotypic and biochemical properties, and phylogenetic analysis placed them in separate well-supported clades within the genus. Overall, our results demonstrate that multiple plant-pathogenic Clostridium species can cause soft rot disease on sweetpotato and suggest that a variety of other plant hosts may also be susceptible.

Progress Towards Bioelectrochemical Remediation of Hexavalent Chromium

Chromium is one of the most frequently used metal contaminants. Its hexavalent form Cr(VI), which is exploited in many industrial activities, is highly toxic, is water-soluble in the full pH range, and is a major threat to groundwater resources. Alongside traditional approaches to Cr(VI) treatment based on physical-chemical methods, technologies exploiting the ability of several microorganisms to reduce toxic and mobile Cr(VI) to the less toxic and stable Cr(III) form have been developed to improve the cost-effectiveness and sustainability of remediating hexavalent chromium-contaminated groundwater. Bioelectrochemical systems (BESs), principally investigated for wastewater treatment, may represent an innovative option for groundwater remediation. By using electrodes as virtually inexhaustible electron donors and acceptors to promote microbial oxidation-reduction reactions, in in situ remediation, BESs may offer the advantage of limited energy and chemicals requirements in comparison to other bioremediation technologies, which rely on external supplies of limiting inorganic nutrients and electron acceptors or donors to ensure proper conditions for microbial activity. Electron transfer is continuously promoted/controlled in terms of current or voltage application between the electrodes, close to which electrochemically active microorganisms are located. Therefore, this enhances the options of process real-time monitoring and control, which are often limited in in situ treatment schemes. This paper reviews research with BESs for treating chromium-contaminated wastewater, by focusing on the perspectives for Cr(VI) bioelectrochemical remediation and open research issues.

Anaerobic reduction of europium by a Clostridium strain as a strategy for rare earth biorecovery

The biorecovery of europium (Eu) from primary (mineral deposits) and secondary (mining wastes) resources is of interest due to its remarkable luminescence properties, important for modern technological applications. In this study, we explored the tolerance levels, reduction and intracellular bioaccumulation of Eu by a site-specific bacterium, Clostridium sp. 2611 isolated from Phalaborwa carbonatite complex. Clostridium sp. 2611 was able to grow in minimal medium containing 0.5 mM Eu³⁺. SEM-EDX analysis confirmed an association between Eu precipitates and the bacterium, while TEM-EDX analysis indicated intracellular accumulation of Eu. According to the HR-XPS analysis, the bacterium was able to reduce Eu³⁺ to Eu²⁺ under growth and non-growth conditions. Preliminary protein characterization seems to indicate that a cytoplasmic pyruvate oxidoreductase is responsible for Eu bioreduction. These findings suggest the bioreduction of Eu³⁺ by Clostridium sp. as a resistance mechanism, can be exploited for the biorecovery of this metal.

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.

Faecal bacterial communities from Mediterranean loggerhead sea turtles (Caretta caretta)

The loggerhead sea turtle (Caretta caretta) is the most widespread sea turtle species in the Mediterranean Sea and a relevant pollution 'flagship species'. Here, we profiled the faecal microbiota from 29 C. caretta from a rescue centre, and explored the impact of several variables linked to both the animal itself and the environment (i.e., tank water ecosystem). We show that loggerhead turtles share more gut microbiota features with carnivorous marine mammals, than with phylogenetically close, but herbivorous, turtles, as a confirmation of the gut microbiota adaptive function to diet and environment. We also highlight a relation between the microbiota composition and the size (and consequently the age) of the turtles. Finally, we point out that the gut microbiota of sea turtles shows unexpectedly low exchange of microbes with the aquatic environment and is resilient to the stress induced by short-time captivity.

Clostridium neonatale sp. nov. linked to necrotizing enterocolitis in neonates and a clarification of species assignable to the genus Clostridium (Prazmowski 1880) emend. Lawson and Rainey 2016

A description of an outbreak of necrotizing enterocolitis among neonates, linked to the putative novel species Clostridium neonatale and assignable to the genus Clostridium, was previously reported in brief but that name had never been validly published (Alfa et al. Clin Inf Dis 2002;35:S101-S105). Features of this taxon group and its phylogenetic position with respect to contemporary species in the genus Clostridium were recently reviewed and still found to be unique. Therefore, we provide here a description based on biochemical, chemotaxonomic and antimicrobial susceptibility testing (AST), matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, 16S rRNA gene sequencing as well as information obtained by whole genome sequencing (WGS) for strains 99A005^T and 99A006. Those two C. neonatale strains were essentially identical to each other, with genome sizes of 4 658 596-4 705 520 bp and G+C content of 28.4-28.5 mol% (WGS). AST inferred susceptibility to 14 antibiotics. MALDI-TOF spectra were unique and could potentially be used for identification. The type strain is (NML) LCDC 99A005^T [=ATCC BAA-265^T=CCUG 46077^T=St. Boniface Hospital 30686^T]. While performing this review, we found that the names of 24 validly published species assignable to the genus Clostridium had been omitted from the emended description of the genus (Lawson and Rainey Int J Syst Evol Microbiol 2016;66 :1009-1016). Those species are listed in brief here. Lastly, based on this review, we also propose that Eubacterium budayi, Eubacterium nitritogenes and Eubacterium combesii be transferred to the emended genus Clostridium, as Clostridium budayi comb. nov., Clostridium nitritogenes comb. nov. and Clostridium combesii comb. nov., respectively.

First Insights into the Genome of the Cr(VI)-Reducing Bacterium Clostridium chromiireducens DSM 23318

Clostridium chromiireducens is an obligate, anaerobic, Gram-positive, rod-shaped, and spore-forming bacterium that is able to reduce Cr(VI). The draft genome consists of one chromosome (5,448 Mb) and contains 4,773 predicted protein-encoding genes.

Clostridium oryzae sp. nov., from soil of a Japanese rice field

An obligately anaerobic bacterial strain designated KC3(T) was isolated from a rice straw-degrading culture, for which soil of a Japanese rice field was used as the inoculum. Cells of strain KC3(T) were determined to be non-cellulolytic, Gram-stain-positive, non-motile, ellipsoidal, spore-forming rods, 0.8-1×4-25 µm. Endospores were formed at a terminal position in elongated cells (12-25 µm, mean 15 µm). The temperature range for growth was 20-50 °C, with an optimum at 37 °C. The pH range for growth was 5.0-7.5, with an optimum at pH 6.0 (slightly acidophilic). Strain KC3(T) fermented cellobiose to lactate, butyrate, acetate, formate, hydrogen and carbon dioxide. The major cellular fatty acids (>10 %) were C14 : 0, C16 : 0 and C19 : 0 cyclo 11,12 dimethylacetal. The DNA G+C content of strain KC3(T) was 37.5 mol%. 16S rRNA gene sequence analysis revealed that strain KC3(T) shared low sequence similarity (<93 %) with type strains of the genus Clostridium sensu stricto (Clostridium rRNA cluster I). Analyses of the DNA gyrase A and ATP synthase beta subunit sequences supported the affiliation of strain KC3(T) to the genus Clostridium sensu stricto. The evidence presented here indicates that strain KC3(T) represents a novel species of the genus Clostridium, for which the name Clostridium oryzae sp. nov. is proposed. The type strain of Clostridium oryzae is KC3(T) ( = DSM 28571(T) = NBRC 110163(T)).

Clostridium algifaecis sp. nov., an anaerobic bacterial species from decomposing algal scum

Two anaerobic bacterial strains, MB9-7(T) and MB9-9, were isolated from decomposing algal scum and were characterized using a polyphasic approach. Phylogenetic analysis of 16S rRNA gene sequences showed that strains MB9-7(T) and MB9-9 are closely related to each other (99.7% similarity) and they are also closely related to Clostridium tyrobutyricum (96.5%). The two strains were Gram-stain positive and rod-shaped. Growth occurred at 20-45 °C, at pH 4.0-8.0 and at NaCl concentrations of up to 2% (w/v). Acid was produced from glucose, xylose and mannose. Products of fermentation in PYG medium were mainly butyrate, acetate, carbon dioxide and hydrogen. The predominant cellular fatty acids were C(14:0) and C(16:0). The cellular polar lipids comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two glycolipids, one phospholipid, one aminophospholipid and two aminolipids. The DNA G+C contents of strain MB9-7(T) and MB9-9 were 27.9 and 28.7 mol%, respectively. These results support the assignment of the new isolates to the genus Clostridium and also distinguish them from other species of the genus Clostridium. Hence, it is proposed that strains MB9-7(T) and MB9-9 represent a novel species of the genus Clostridium, with the suggested name Clostridium algifaecis sp. nov. The type strain is MB9-7(T) ( =CGMCC 1.5188(T) =DSM 28783(T)).

Effect of metal oxide nanoparticles on microbial community structure and function in two different soil types

Increased availability of nanoparticle-based products will, inevitably, expose the environment to these materials. Engineered nanoparticles (ENPs) may thus find their way into the soil environment via wastewater, dumpsters and other anthropogenic sources; metallic oxide nanoparticles comprise one group of ENPs that could potentially be hazardous for the environment. Because the soil bacterial community is a major service provider for the ecosystem and humankind, it is critical to study the effects of ENP exposure on soil bacteria. These effects were evaluated by measuring bacterial community activity, composition and size following exposure to copper oxide (CuO) and magnetite (Fe₃O₄) nanosized (<50 nm) particles. Two different soil types were examined: a sandy loam (Bet-Dagan) and a sandy clay loam (Yatir), under two ENP concentrations (1%, 0.1%). Results indicate that the bacterial community in Bet-Dagan soil was more susceptible to change due to exposure to these ENPs, relative to Yatir soil. More specifically, CuO had a strong effect on bacterial hydrolytic activity, oxidative potential, community composition and size in Bet-Dagan soil. Few effects were noted in the Yatir soil, although 1% CuO exposure did cause a significant decreased oxidative potential and changes to community composition. Fe₃O₄ changed the hydrolytic activity and bacterial community composition in Bet-Dagan soil but did not affect the Yatir soil bacterial community. Furthermore, in Bet-Dagan soil, abundance of bacteria annotated to OTUs from the Bacilli class decreased after addition of 0.1% CuO but increased with 1% CuO, while in Yatir soil their abundance was reduced with 1% CuO. Other important soil bacterial groups, including Rhizobiales and Sphingobacteriaceae, were negatively affected by CuO addition to soil. These results indicate that both ENPs are potentially harmful to soil environments. Furthermore, it is suggested that the clay fraction and organic matter in different soils interact with the ENPs and reduce their toxicity.