Effect of temperature on the reductive dechlorination of 1,2,3,4-tetrachlorodibenzofuran in anaerobic PCDD/F-contaminated sediments

The effect of temperature on the reductive dechlorination in sediments of the PCDD/F-contaminated Kymijoki River, Finland was assessed with 1,2,3,4-tetrachlorodibenzofuran (1,2,3,4-TeCDF) at various temperatures and with co-amendment of 2,3,4,6-tetrachlorophenol (2,3,4,6-TeCP) in laboratory microcosms. The dechlorination rate of 1,2,3,4-TeCDF increased with incubation temperature, with TeCDF half-lives of 2.1 y at 21°C, 3.9 y at 15°C, and 19.0 y at 4°C. Co-amendment with 2,3,4,6-TeCP reduced the TeCDF half-life to 1.8 y at 21°C. 1,2,3,4-TeCDF was dechlorinated mainly in the lateral position to 1,3,4-TrCDF and then to 1,3-DiCDF over 29 months, but incubation temperature affected the relative molar ratios of the dechlorination products. The abundance of the Dehalococcoides-like Chloroflexi community did not substantially change in microcosms over 24 months incubation at the different temperatures. The dechlorination activity of 1,2,3,4-TeCDF was significantly limited at lower temperatures, which should be considered in predicting the environmental fate of aged PCDD/Fs in sediments of the Kymijoki River.

Complete genome sequence of Granulicella tundricola type strain MP5ACTX9(T), an Acidobacteria from tundra soil

Granulicella tundricola strain MP5ACTX9(T) is a novel species of the genus Granulicella in subdivision 1 Acidobacteria. G. tundricola is a predominant member of soil bacterial communities, active at low temperatures and nutrient limiting conditions in Arctic alpine tundra. The organism is a cold-adapted acidophile and a versatile heterotroph that hydrolyzes a suite of sugars and complex polysaccharides. Genome analysis revealed metabolic versatility with genes involved in metabolism and transport of carbohydrates, including gene modules encoding for the carbohydrate-active enzyme (CAZy) families for the breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides such as plant based carbon polymers. The genome of G. tundricola strain MP5ACTX9(T) consists of 4,309,151 bp of a circular chromosome and five mega plasmids with a total genome content of 5,503,984 bp. The genome comprises 4,705 protein-coding genes and 52 RNA genes.

Most influential FEMS publications

A selection of influential FEMS publications to celebrate the 40th anniversary of FEMS.

Genome sequence of the anaerobic bacterium Bacillus sp. strain ZYK, a selenite and nitrate reducer from paddy soil

Bacillus sp. strain ZYK, a member of the phylum Firmicutes, is of interest for its ability to reduce nitrate and selenite and for its resistance to arsenic under anaerobic conditions. Here we describe some key features of this organism, together with the complete genome sequence and annotation. The 3,575,797 bp long chromosome with its 3,454 protein-coding and 70 RNA genes, and the information gained from its sequence will be relevant to the elucidation of microbially-mediated transformations of nitrogen, selenium and arsenic in paddy soil.

Anaerobic reductive dechlorination of 1,2,3,4-tetrachlorodibenzofuran in polychlorinated dibenzo-p-dioxin- and dibenzofuran-contaminated sediments of the Kymijoki River, Finland

Sediments of the Kymijoki River are highly contaminated with polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs). These persistent PCDD/Fs resist biotic degradation and therefore the potential for microbial reductive dechlorination was assessed to determine how microbes impact the fate of these compounds. Anaerobic sediment microcosms of five different sites in the river were spiked with 1,2,3,4-tetrachlorodibenzofuran (1,2,3,4-TeCDF) as a model compound to determine the dechlorination potential in the sediments. Dechlorinating bacteria were active in all the study sites of the river. The extent of dechlorination over 10 and 29 months corresponded to the levels of aged PCDD/Fs, with sediments of the most contaminated site at Kuusankoski being the most active for reductive dechlorination. The dechlorination activity and levels of aged PCDD/Fs were correlated within the sediment cores at the all sites. The pathway of 1,2,3,4-TeCDF dechlorination was mainly via 1,3,4-trichlorodibenzofuran (TrCDF) to 1,3-dichlorodibenzofuran (DiCDF). Dechlorination via 1,2,4-TrCDF to further dechlorination products was also detected. Lateral reductive dechlorination would decrease the toxicity of 2,3,7,8-substituted PCDD/Fs. Our data suggest that sediments of the Kymijoki River contain indigenous microorganisms that are responsible for dechlorination of PCDD/Fs, especially at the most contaminated site.

Enriching for microbial reductive dechlorination of polychlorinated dibenzo-p-dioxins and dibenzofurans

Anaerobic enrichment cultures derived from contaminated Kymijoki River sediments dechlorinated 1,2,3,4-tetrachlorodibenzofuran (1,2,3,4-tetra-CDF), octachlorodibenzofuran (octa-CDF) and 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-tetra-CDD). 1,2,3,4-tetra-CDF was dechlorinated via 1,2,3-, 2,3,4-, and 1,3,4/1,2,4-tri-CDFs to 1,3-, 2,3-, and 2,4-di-CDFs and finally to 4-mono-CDF. The dechlorination rate of 1,2,3,4-tetra-CDF was generally slower than that of 1,2,3,4-tetra-CDD. The rate and extent of 1,2,3,4-tetra-CDD dechlorination was enhanced by addition of pentachloronitrobenzene (PCNB) as a co-substrate. Dechlorination of spiked octa-CDF was observed with the production of hepta-, hexa-, penta- and tetra-CDFs over 6 months. Two major phylotypes of the Chloroflexi community showed an increase, one of which was identical to the Dehalococcoides mccartyi Pinellas subgroup. A set of twelve putative reductive dehalogenase (rdh) genes increased in abundance with addition of 1,2,3,4-tetra-CDF, 1,2,3,4-tetra-CDD and/or PCNB. This information will aid in understanding how indigenous microbial communities impact the fate of PCDFs and in developing strategies for bioremediation of PCDD/F contaminated sediments.

Complete genome sequence of Granulicella mallensis type strain MP5ACTX8(T), an acidobacterium from tundra soil

Granulicella mallensis MP5ACTX8(T) is a novel species of the genus Granulicella in subdivision 1of Acidobacteria. G. mallensis is of ecological interest being a member of the dominant soil bacterial community active at low temperatures and nutrient limiting conditions in Arctic alpine tundra. G. mallensis is a cold-adapted acidophile and a versatile heterotroph that hydrolyzes a suite of sugars and complex polysaccharides. Genome analysis revealed metabolic versatility with genes involved in metabolism and transport of carbohydrates. These include gene modules encoding the carbohydrate-active enzyme (CAZyme) family involved in breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides including plant based carbon polymers. The genome of Granulicella mallensis MP5ACTX8(T) consists of a single replicon of 6,237,577 base pairs (bp) with 4,907 protein-coding genes and 53 RNA genes.

Seleniivibrio woodruffii gen. nov., sp. nov., a selenate- and arsenate-respiring bacterium in the Deferribacteraceae

A Gram-type-negative, obligately anaerobic, selenate-respiring bacterium, strain S4T, was isolated from activated sludge of a wastewater treatment plant in New Jersey after enrichment with 10 mM selenate as the sole electron acceptor. In addition to its selenate-respiring capability, strain S4T also respired arsenate with acetate as carbon source and electron donor. Fermentative growth was not observed. The optimum growth temperature was 37 °C and optimum pH was pH 7. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain S4T is a novel member of the family Deferribacteraceae , with the type strain of Denitrovibrio acetiphilus as its closest cultivated relative, with 91.5 % sequence similarity. The cellular fatty acid profile was composed predominantly of straight-chain fatty acids C14 : 0, C15 : 0, C16 : 0, C17 : 0 and C18 : 0, which distinguishes this organism from its closest relatives. The DNA G+C content was 47.7 mol%. Together, these findings support the conclusion that strain S4T represents a novel genus and species, for which the name Seleniivibrio woodruffii gen. nov., sp. nov. is proposed. The type strain of Seleniivibrio woodruffii is S4T ( = DSM 24984T = ATCC BAA-2290T).

Microbially mediated reductive dechlorination of weathered polychlorinated dibenzofurans in Kymijoki sediment mesocosms

Little is known about the potential for indigenous microorganisms to reductively dechlorinate weathered polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs) in contaminated sediments. The sediments of River Kymijoki, Finland are heavily contaminated with PCDFs originating from manufacture of the chlorophenol-based fungicide Ky-5. Reductive dechlorination of weathered PCDFs was monitored to examine strategies for stimulating such activities. Amendments with electron donors, a halogenated co-substrate (tetrachlorobenzene, TeCBz), and bioaugmentation with a mixed culture containing Dehalococcoides mccartyi strain 195 were used to stimulate dechlorination activity in 30 L River Kymijoki sediment mesocosms incubated from 18 °C to 21 °C. An initial onset of dechlorination of octa-, hepta- and hexa-CDFs was observed in all mesocosms in the first 2 years of incubation. During this initial 2-year period, the decrease in the mol% contribution of these PCDFs was coupled with an increase in the mol% contribution of tetra- and penta-CDFs. The ratio of 1,2,3,4,6,7,8- to 1,2,3,4,6,8,9-hepta-CDF increased significantly. Subtle differences were observed between amended and unamended mesocosms. For penta-CDFs, a decreasing mol% ratio of peri vs. total chlorines and increasing mol% ratio of lateral vs. total chlorines was observed in mesocosms amended with TeCBz, suggesting that the amendments may affect pathways of dechlorination. Analysis of congener patterns using principal components analysis supported the observation that dechlorination was most pronounced during the first 2 years. Polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) analysis of 16S rRNA genes revealed a diverse Chloroflexi community. This study showed evidence for dechlorination of weathered PCDFs in Kymijoki sediment mesocosms mediated by indigenous microorganisms.

Complete genome sequence of Terriglobus saanensis type strain SP1PR4(T), an Acidobacteria from tundra soil

Terriglobus saanensis SP1PR4(T) is a novel species of the genus Terriglobus. T. saanensis is of ecological interest because it is a representative of the phylum Acidobacteria, which are dominant members of bacterial soil microbiota in Arctic ecosystems. T. saanensis is a cold-adapted acidophile and a versatile heterotroph utilizing a suite of simple sugars and complex polysaccharides. The genome contained an abundance of genes assigned to metabolism and transport of carbohydrates including gene modules encoding for carbohydrate-active enzyme (CAZyme) family involved in breakdown, utilization and biosynthesis of diverse structural and storage polysaccharides. T. saanensis SP1PR4(T) represents the first member of genus Terriglobus with a completed genome sequence, consisting of a single replicon of 5,095,226 base pairs (bp), 54 RNA genes and 4,279 protein-coding genes. We infer that the physiology and metabolic potential of T. saanensis is adapted to allow for resilience to the nutrient-deficient conditions and fluctuating temperatures of Arctic tundra soils.

Chronic laminitis is associated with potential bacterial pathogens in the laminae

A common sequella of chronic laminitis in horses is repeated abscesses with variable lameness and drainage. It is unclear whether the exudate represents the debridement phase of a non-septic inflammatory process involving clearance of laminar tissue damaged during the acute episode of laminitis, or a response to a microbial infection developed by ascent of microbes from the environment to the tissue via the white line. The objective of this study was to evaluate the possibility that an undiagnosed microbial infection in laminar tissue is present in laminar tissue collected from chronically laminitic horses without an active hoof abscess. Methods to collect laminar tissue, aseptically, from control (non-laminitic) horses and those with chronic/recurrent laminitis are described. Laminae homogenates were evaluated for the presence of bacteria. Bacteria were identified using biochemical tests and sequencing of 16S rRNA and virulence genes. Laminae from chronically laminitic horses revealed 100-fold higher levels (P=0.002) of bacteria compared to control, non-laminitic horses. Although environmental organisms were identified, potential pathogens were identified. Included were Gram positive bacteria, Brevibacterium luteolum, coagulase-negative Staphylococcus spp. as well as Gram negative bacteria, enterohemorrhagic Escherichia coli and Alcaligenes faecalis. Further research is warranted to evaluate the role of bacteria in equine chronic laminitis.

Granulicella arctica sp. nov., Granulicella mallensis sp. nov., Granulicella tundricola sp. nov. and Granulicella sapmiensis sp. nov., novel acidobacteria from tundra soil

Four aerobic bacteria, designated MP5ACTX2(T), MP5ACTX8(T), MP5ACTX9(T) and S6CTX5A(T), were isolated from tundra soil of north-western Finland (69° 03' N 20° 50' E). Cells of all isolates were Gram-negative, non-motile rods. Phylogenetic analysis indicated that they belonged to the genus Granulicella of subdivision 1 of the phylum Acidobacteriahttp://dx.doi.org/10.1601/nm.7918. 16S rRNA gene sequence similarity between the new isolates and the type strains of Granulicella aggregans, Granulicella paludicola, Granulicella pectinivorans and Granulicella rosea ranged from 94 to 99 %. Analysis of the RNA polymerase beta subunit (rpoB) gene sequence indicated that the isolates represented novel species of the genus Granulicella (<92 % rpoB sequence similarity between the isolates and members of the genus Granulicella). This was also confirmed by low DNA-DNA relatedness (31 %) between strain S6CTX5A(T) and the type strain of G. pectinivorans, which exhibited 99.1 % 16S rRNA gene sequence similarity and 91.7 % rpoB gene sequence similarity. The isolates grew at pH 3.5-6.5 and at 4-26 °C. Sugars were the preferred growth substrates. The major cellular fatty acids were iso-C(15 : 0), C(16 : 1)ω7c and C(16 : 0) and the major isoprenoid quinone was MK-8. The DNA G+C content was 56-60 mol%. On the basis of phylogenetic analysis and chemotaxonomic and physiological data, the isolates represent four novel species of the genus Granulicella, for which the names Granulicella arctica MP5ACTX2(T) (= ATCC BAA-1858(T) = DSM 23128(T)), Granulicella mallensis MP5ACTX8(T) (= ATCC BAA-1857(T) = DSM 23137(T)), Granulicella tundricola MP5ACTX9(T) (ATCC BAA-1859(T) = DSM 23138(T)) and Granulicella sapmiensis S6CTX5A(T) (= LMG 26174(T) = DSM 23136(T)) are proposed. An emended description of the genus Granulicella is also presented.

Microbially mediated O-methylation of bisphenol A results in metabolites with increased toxicity to the developing zebrafish (Danio rerio) embryo

Bisphenol A (BPA) is used in the manufacture of plastics, and has been identified in various environmental matrices, including human serum and breast milk. The prevalence of BPA in the environment and the potential exposure to humans underscores the need to more fully understand the fate of BPA in the environment and the resulting effects and toxicity to humans and other organisms. Here we demonstrate that Mycobacterium species, including Mycobacterium vanbaalenii strain PYR-1, are able to O-methylate BPA to its mono- and dimethyl ether derivatives (BPA MME and BPA DME, respectively). The O-methylation of BPA results in metabolites with increased toxicity as shown from differences in survival and occurrence of developmental lesions in developing zebrafish embryos exposed to BPA, BPA MME, and BPA DME. The mono- and dimethyl ether derivatives were more toxic than BPA, resulting in increased mortality at 5 (LC(50) = 0.66 and 1.2 mg L(-1)) and 28 (LC(50) = 0.38, <0.5 mg L(-1)) days post fertilization. Furthermore, exposure to either of the O-methylated metabolites resulted in an increase in the incidence of developmental lesions as compared to BPA exposure. These data illustrate a new mechanism for microbial transformation of BPA, producing metabolites warranting further study to understand their prevalence and effects in the environment.

Kangiella spongicola sp. nov., a halophilic marine bacterium isolated from the sponge Chondrilla nucula

A novel halophilic bacterium of the genus Kangiella was isolated from a marine sponge collected from the Florida Keys, USA. Strain A79T, an aerobic, Gram-negative, non-motile, rod-shaped bacterium, grew in 2–15 % (w/v) NaCl, at a temperature of 10–49 °C and at pH 4.5–10. Phylogenetic analysis placed strain A79T in the family Alcanivoraceae in the class Gammaproteobacteria. Strain A79T showed 98.5 % 16S rRNA gene sequence similarity to Kangiella japonica KMM 3899T, 96.6 % similarity to Kangiella koreensis DSM 16069T and 95.6 % similarity to Kangiella aquimarina DSM 16071T. The major cellular fatty acids were iso-C11 : 0, iso-C11 : 0 3-OH, iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c and the G+C content of the genomic DNA was 44.9 mol%. On the basis of physiological, chemotaxonomic and phylogenetic comparisons, strain A79T represents a novel species in the genus Kangiella, for which the name Kangiella spongicola sp. nov. is proposed. The type strain is A79T ( = ATCC BAA-2076T = DSM 23219T).

Desulfurispirillum indicum sp. nov., a selenate- and selenite-respiring bacterium isolated from an estuarine canal

Strain S5T, a novel bacterium that was isolated for its capability to respire selenate to elemental selenium, is described. In addition to selenate respiration, it was also capable of dissimilatory selenite, arsenate and nitrate reduction with short-chain organic acids such as pyruvate, lactate and acetate as the carbon sources and electron donors. The isolate was unable to grow fermentatively. Strain S5T was isolated from sediment of an estuarine canal in Chennai, India. Phylogenetic analysis of the 16S rRNA gene of this novel isolate revealed that it belonged to the family Chrysiogenaceae with sequence similarities of 92 and 98 %, respectively, with the type strains of Chrysiogenes arsenatis and Desulfurispirillum alkaliphilum, its closest known relatives. Strain S5T and D. alkaliphilum were closely related in terms of their 16S rRNA gene phylogeny; however, they varied greatly in their genomic DNA G+C content (56 mol% versus 45 mol%) and cellular fatty acid compositions, as well as in many metabolic capabilities. Strain S5T represents a novel species for which the name Desulfurispirillum indicum sp. nov. is proposed; the type strain is S5T (=DSM 22839T =ATCC BAA-1389T).

Terriglobus saanensis sp. nov., an acidobacterium isolated from tundra soil

Two aerobic bacterial strains, designated SP1PR4(T) and SP1PR5, were isolated from tundra soil samples collected from Saana fjeld, North-western Finland (69° 03' N 20° 50' E). Cells of both strains were Gram-negative, non-motile rods. Phylogenetic analysis indicated that the strains belong to the genus Terriglobus in subdivision 1 of the phylum Acidobacteria. Strains SP1PR4(T) and SP1PR5 shared identical BOX and ERIC fingerprints and 99.7 % 16S rRNA gene similarity indicating that, together with their identical physiological features, these strains are members of the same species. The 16S rRNA gene sequence similarity of SP1PR4(T) and SP1PR5 with Terriglobus roseus DSM 18391(T) was 97.1 %. A low DNA-DNA hybridization value (<20 %) and rpoB gene sequence similarity (83.6 %) with T. roseus DSM 18391(T) indicated that the tundra soil isolates represent novel members of the genus Terriglobus. Strains SP1PR4(T) and SP1PR5 grew at pH 4.5-7.5 and 4-30 °C. Sugars were the preferred growth substrates. The major cellular fatty acids were iso-C(15 : 0), C(16 : 1)ω7c, iso-C(13 : 0) and C(16 : 0). The DNA G+C content of strain SP1PR4(T) was 57.3 mol%. Based on phylogenetic, chemotaxonomic and physiological analyses, the name Terriglobus saanensis sp. nov. is proposed to accommodate the two strains; the type strain is SP1PR4(T) ( = DSM 23119(T)  = ATCC BAA-1853(T)).

Embryonic exposure to tetrabromobisphenol A and its metabolites, bisphenol A and tetrabromobisphenol A dimethyl ether disrupts normal zebrafish (Danio rerio) development and matrix metalloproteinase expression

Tetrabromobisphenol A (TBBPA) is a widely used brominated flame retardant that is persistent in the environment and detected in human serum and breast milk. TBBPA is microbiologically transformed in anaerobic environments to bisphenol A (BPA) and in aerobic environments to TBBPA dimethyl ether (TBBPA DME). Despite the detection of TBBPA DME in the environment, the resulting toxicity is not known. The relative toxicity of TBBPA, BPA and TBBPA DME was determined using embryonic exposure of zebrafish, with BPA and TBBPA DME exhibiting lower potency than TBBPA. TBBPA exposure resulted in 100% mortality at 3 (1.6mg/L) and 1.5μM (0.8mg/L), whereas BPA and TBBPA DME did not result in significant embryonic mortality in comparison to controls. While all three caused edema and hemorrhage, only TBBPA specifically caused decreased heart rate, edema of the trunk, and tail malformations. Matrix metalloproteinase (MMP) expression was measured due to the role of these enzymes in the remodeling of the extracellular matrix during tissue morphogenesis, wound healing and cell migration. MMP-2, -9 and -13 expression increased (2-8-fold) after TBBPA exposure followed by an increase in the degradation of collagen I and gelatin. TBBPA DME exposure resulted in only a slight increase (less than 2-fold) in MMP expression and did not significantly increase enzymatic activity. These data suggest that TBBPA is more potent than BPA or TBBPA DME and indicate that the trunk and tail phenotypes seen after TBBPA exposure could be due in part to alteration of proper MMP expression and activity.

Mucilaginibacter frigoritolerans sp. nov., Mucilaginibacter lappiensis sp. nov. and Mucilaginibacter mallensis sp. nov., isolated from soil and lichen samples

Five cold-adapted bacteria belonging to the genus Mucilaginibacter were isolated from lichen and soil samples collected from Finnish Lapland and investigated in detail by phenotypic and phylogenetic analyses. Based on 16S rRNA gene phylogeny, the novel strains represent three new branches within the genus Mucilaginibacter. The strains were aerobic, chemo-organotrophic, non-motile rods and formed pigmented, smooth, mucoid colonies on solid media. The strains grew between 0 and 33 °C (optimum growth at 25 °C) and at pH 4.5-8.0 (optimum growth at pH 6.0). The main cellular fatty acids were iso-C(15 : 0), summed feature 3 (C(16 : 1)ω7c/iso-C(15 : 0) 2-OH) and iso-C(17 : 0) 3-OH and the major respiratory quinone was MK-7. The DNA G+C contents were 44.0-46.5&emsp14;mol%. Based on phylogenetic, phenotypic and chemotaxonomic data, the strains represent three novel species of the genus Mucilaginibacter for which the names Mucilaginibacter frigoritolerans sp. nov. (type strain FT22(T) =ATCC BAA-1854(T) =LMG 25359(T)), Mucilaginibacter lappiensis sp. nov. (type strain ANJLI2(T) =ATCC BAA-1855(T) =LMG 25358(T)) and Mucilaginibacter mallensis sp. nov. (type strain MP1X4(T) =ATCC BAA-1856(T) =LMG 25360(T)) are proposed.