Geomycology: biogeochemical transformations of rocks, minerals, metals and radionuclides by fungi, bioweathering and bioremediation

Antagonistic fungi, trichoderma spp.: panoply of biological control

Arsenic in the environment: Biology and Chemistry

The higher ranks of the class Actinobacteria were proposed and described in 1997. At each rank, the taxa were delineated from each other solely on the basis of 16S rRNA gene sequence phylogenetic clustering and taxon-specific 16S rRNA signature nucleotides. In the past 10 years, many novel members have been assigned to this class while, at the same time, some members have been reclassified. The new 16S rRNA gene sequence information and the changes in phylogenetic positions of some taxa influence decisions about which 16S rRNA nucleotides to define as taxon-specific. As a consequence, the phylogenetic relationships of Actinobacteria at higher levels may need to be reconstructed. Here, we present new 16S rRNA signature nucleotide patterns of taxa above the family level and indicate the affiliation of genera to families. These sets replace the signatures published in 1997. In addition, Actinopolysporineae subord. nov. and Actinopolysporaceae fam. nov. are proposed to accommodate the genus Actinopolyspora, Kineosporiineae subord. nov. and Kineosporiaceae fam. nov. are proposed to accommodate the genera Kineococcus, Kineosporia and Quadrisphaera, Beutenbergiaceae fam. nov. is proposed to accommodate the genera Beutenbergia, Georgenia and Salana and Cryptosporangiaceae fam. nov. is proposed to accommodate the genus Cryptosporangium. The families Nocardiaceae and Gordoniaceae are proposed to be combined in an emended family Nocardiaceae. Emended descriptions are also proposed for most of the other higher taxa.

An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa.

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

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Genome-Based Taxonomic Classification of the Phylum Actinobacteria

Indigenous fungi isolated from soil of a former gasworks site were investigated in submerged cultures with pyrene as the sole carbon source. Five fungal strains capable of degrading pyrene included one strain of Trichoderma harzianum and four strains with characteristics of the genus Penicillium. These are identified as Penicillium simplicissimum, Penicillium janthinellum, Penicillium funiculosum and Penicillium terrestre. A maximum of 75% of 50 mg l−1 and 67% of 100 mg l−1 of pyrene was removed by the fast degrading strain P. terrestre at 22°C during 28 days of incubation. The slower degrader P. janthinellum was able to remove 57% of 50 mg l−1 and about 31.5% of 100 mg l−1 pyrene. Degradation of pyrene is directly correlated with biomass development. To the best of our knowledge, this is the first time that fungi have been reported to use pyrene as the sole carbon and energy source. They may be ideal candidates for effective bioremediation of polycyclic aromatic hydrocarbons.

Degradation of pyrene by indigenous fungi from a former gasworks site

An unknown Gram-positive, catalase-positive, facultatively anaerobic, non-spore-forming, coccus-shaped bacterium originating from sediment was characterized using phenotypic, molecular chemical and molecular phylogenetic methods. Chemical studies revealed the presence of a cell-wall murein based on ll-diaminopimelic acid (type ll-Dpm-glycine1), a complex mixture of saturated, monounsaturated and iso- and anteiso-methyl-branched, non-hydroxylated, long-chain cellular fatty acids and tetrahydrogenated menaquinones with eight isoprene units [MK-8(H4)] as the major respiratory lipoquinone. This combination of characteristics somewhat resembled members of the suborder Micrococcineae, but did not correspond to any currently described species. Comparative 16S rRNA gene sequencing confirmed that the unidentified coccus-shaped organism is a member of the Actinobacteria and represents a hitherto-unknown subline related to, albeit different from, a number of taxa including Intrasporangium, Janibacter, Terrabacter, Terracoccus and Ornithinicoccus. Based on phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium originating from lake sediment be classified as a new genus and species, Arsenicicoccus bolidensis gen. nov., sp. nov. (type strain CCUG 47306T=DSM 15745T).

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Arsenicicoccus bolidensis gen. nov., sp. nov., a novel actinomycete isolated from contaminated lake sediment

Arsenic remobilization from sediments contaminated with mine tailings near the Adak mine in Västerbotten district (northern Sweden)

Arsenicicoccus bolidensis a novel arsenic reducing actinomycete in contaminated sediments near the Adak mine (northern Sweden): impact on water chemistry.

Possible biological mechanisms contributing towards the transformation of arsenic (As) in aquifer sediments was investigated in Ambikanagar. Enrichment cultures indicated several As tolerant species, which actively reduced As(V) under sub-oxic conditions. High As concentrations in the microcosms increased toxicity, and hence, bacterial types and the heterotrophic plate counts declined. Bacteria isolated from enrichment cultures were Acinetobacter johnsonii, Citrobacter freundii, Comamonas testosteroni, Enterobacter cloacae, and Sphingobium yanoikuyae. On inoculating the medium with these bacteria, different growth and As(V) reduction rates occurred. A zero-order model fits the As(V) reduction data. Initial As concentration seems to affect growth and As(V) reduction rates, and these values were highest in A. johnsonii. In contrast, C. testosteroni and S. yanoikuyae were almost unaffected by the initial As(V) concentrations. As(V) reduction in these bacteria occurs for detoxification or respiratory purposes (e.g., A. johnsonii). These experiments confirm that microorganisms may result in remobilization of As from sediments, and impact groundwater treatment.

Ambujom Saraswathy

Papers

Degradation of pyrene by indigenous fungi from a former gasworks site

Arsenicicoccus bolidensis gen. nov., sp. nov., a novel actinomycete isolated from contaminated lake sediment

Arsenic remobilization from sediments contaminated with mine tailings near the Adak mine in Västerbotten district (northern Sweden)

Arsenicicoccus bolidensis a novel arsenic reducing actinomycete in contaminated sediments near the Adak mine (northern Sweden): impact on water chemistry.

Arsenic reduction by indigenous bacteria in shallow aquifers from Ambikanagar, West Bengal, India