Effect of Growth Media on the Diversity of Neocallimastigomycetes from Non-Rumen Habitats.

Anaerobic fungi (AF), belonging to the phylum Neocallimastigomycota, are a pivotal component of the digestive tract microbiome of various herbivorous animals. In the last decade, the diversity of AF has rapidly expanded due to the exploration of numerous (novel) habitats. Studies aiming at understanding the role of AF require robust and reliable isolation and cultivation techniques, many of which remained unchanged for decades. Using amplicon sequencing, we compared three different media: medium with rumen fluid (RF), depleted rumen fluid (DRF), and no rumen fluid (NRF) to enrich the AF from the feces of yak, as a rumen control; and Przewalski's horse, llama, guanaco, and elephant, as a non-rumen habitats. The results revealed the selective enrichment of Piromyces and Neocallimastix from the feces of elephant and llama, respectively, in the RF medium. Similarly, the enrichment culture in DRF medium explicitly manifested Piromyces-related sequences from elephant feces. Five new clades (MM1-5) were defined from llama, guanaco, yak, and elephant feces that could as well be enriched from llama and elephant samples using non-conventional DRF and NRF media. This study presents evidence for the selective enrichment of certain genera in medium with RF and DRF from rumen as well as from non-rumen samples. NRF medium is suggested for the isolation of AF from non-rumen environments.

Desulfovibrio brasiliensis sp. nov., a moderate halophilic sulfate-reducing bacterium from Lagoa Vermelha (Brazil) mediating dolomite formation.

A novel halotolerant sulfate-reducing bacterium, Desulfovibrio brasiliensis strain LVform1, was isolated from sediments of a dolomite-forming hypersaline coastal lagoon, Lagoa Vermelha, in the state of Rio de Janeiro, Brazil. The cells are vibrio-shaped and 0.30 to 0.45 microm by 1.0 to 3.5 microm in size. These bacteria mediate the precipitation of dolomite [CaMg(CO3)2] in culture experiments. The strain was identified as a member of the genus Desulfovibrio in the delta-subclass of the Proteobacteria on the basis of its 16S rRNA gene sequence, its physiological and morphological properties. Strain LVform1 is obligate sodium-dependent and grows at NaCl concentrations of up to 15%. The 16S rRNA sequence revealed that this strain is closely related to Desulfovibrio halophilus (96.2% similarity) and to Desulfovibrio oxyclinae (96.8% similarity), which were both isolated from Solar Lake, a hypersaline coastal lake in the Sinai, Egypt. Strain LVform1 is barotolerant, growing under pressures of up to 370 bar (37 MPa). We propose strain LVform1 to be the type strain of a novel species of the genus Desulfovibrio, Desulfovibrio brasiliensis (type strain LVform1 = DSMZ No. 15816 and JCM No. 12178). The GenBank/EMBL accession number for the 16S rDNA sequence of strain LVform1 is AJ544687.

Inhibition of anaerobic microbial o-xylene degradation by toluene in sulfidogenic sediment columns and pure cultures.

It is frequently observed in aromatic hydrocarbons such as benzene, toluene, ethylbenzene, xylene (BTEX)-contaminated aquifers that toluene degrades faster than xylenes and benzene. In sediment column experiments which were run with a mixture of BTEX compounds toluene degradation started after a lag period of several weeks. When we omitted toluene from the culture medium o-xylene degradation started. Xylene degradation could be inhibited by adding toluene back to the medium and could be recovered when toluene was omitted again. This was observed repeatedly when toluene concentrations higher than 20 microM were added. Two sulphate-reducing bacterial species, isolated from the column material, were used to investigate the degradation behaviour in detail. Strain TRM1 degraded exclusively toluene, strain OX39 degraded preferentially o-xylene and toluene only after an adaptation period of more than 90 days when added as the sole substrate. Growth and o-xylene degradation of strain OX39 were inhibited by toluene concentrations as low as 40 microM, whereas, in contrast, toluene degradation by strain TRM1 was not inhibited by o-xylene concentrations up to 0.5 mM. Both the column data and the batch experiments indicated that two organisms were responsible for the toluene/xylene degradation in the sediment column. One strain degraded only toluene and was not effected by xylene and the second degraded xylene and was inhibited by toluene. Our findings offer an explanation that the observed differential degradation of BTEX compounds in contaminated aquifers could originate from a partial metabolic inhibition of xylene-degrading organisms by toluene.

Anaerophaga thermohalophila gen. nov., sp. nov., a moderately thermohalophilic, strictly anaerobic fermentative bacterium.

The strictly anaerobic gram-negative bacterium strain Fru22T grows at 50 degrees C in media containing up to 75 g NaCl l(-1). Hexoses and pentoses are fermented to equal molar amounts of acetate, propionate and succinate, and no CO2 is formed. An orange-red pigment similar to flexirrubin is produced during stationary phase upon exposure to light for several days. Cells also produce a surface-active extracellular compound which lowers the surface tension of the medium. This tenside is heat-tolerant up to 70 degrees C and is destroyed by treatment with proteinase K or trypsin, but not by lipase. Comparative 16S rDNA sequence analysis confirmed a phylogenetic affiliation of strain Fru22T to the phylum Bacteroides (Cytophaga/Flavobacterium/Bacteroides), moderately related to the genus Marinilabilia. Therefore, on the basis of phylogenetic, phenotypic and physiological evidence, a new genus, Anaerophaga, is proposed to harbour strain Fru22T (DSM 12881T, OCM 798T) which is described as the type strain of a new species, Anaerophaga thermohalophila gen. nov., sp. nov.