Draft Genome Sequence of Leifsonia poae Strain BS71, Isolated from a Drought Microcosm

We report the draft genome sequence of Leifsonia poae strain BS71. This bacterium was isolated from a low soil moisture content model soil microcosm inoculated with forest soil that had been subject to chronic warming.

Forest Soils—What’s Their Peculiarity?

Mankind expects from forests and forest soils benefits like pure drinking water, space for recreation, habitats for nature-near biocenoses and the production of timber as unrivaled climate-friendly raw material. An overview over 208 recent articles revealed that ecosystem services are actually the main focus in the perception of forest soil functions. Studies on structures and processes that are the basis of forest soil functions and ecosystem services are widely lacking. Therefore, additional literature was included dealing with the distinct soil structure and high porosity and pore continuity of forest soils, as well as with their high biological activity and chemical soil reaction. Thus, the highly differentiated, hierarchical soil structure in combination with the ion exchange capacity and the acid buffering capacity could be described as the main characteristics of forest soils confounding the desired ecosystem services. However, some of these functions of forest soils are endangered under the influence of environmental change or even because of forest management, like mono-cultures or soil compaction through forest machines. In the face of the high vulnerability of forest soils and increased threads, e.g., through soil acidification, it is evident that active soil management strategies must be implemented with the aim to counteract the loss of soil functions or to recover them.

A Putatively New Family of Alphaproteobacterial Chloromethane Degraders from a Deciduous Forest Soil Revealed by Stable Isotope Probing and Metagenomics

Background: Chloromethane (CH3 Cl) is the most abundant halogenated organic compound in the atmosphere and substantially responsible for the destruction of the stratospheric ozone layer. Since anthropogenic CH 3 Cl sources have become negligible with the application of the Montreal Protocol (1987), natural sources, such as vegetation and soils, have increased proportionally in the global budget. CH3 Cl-degrading methylotrophs occurring in soils might be an important and overlooked sink.Results & Conclusions: The objective of our study was to link the biotic CH3 Cl sink with the identity of active microorganisms and their biochemical pathways for CH3 Cl degradation in a deciduous forest soil. When tested in laboratory microcosms, biological CH3 Cl consumption occurred in leaf litter, senescent leaves, and organic and mineral soil horizons. Highest consumption rates, around 2 mmol CH3 Cl g -1 dry weight h -1 , were measured in organic soil and senescent leaves, suggesting that top soil layers are active (micro-)biological CH 3 Cl degradation compartments of forest ecosystems. The DNA of these [13C]-CH3 Cl-degrading microbial communities was labelled using stable isotope probing (SIP), and the corresponding taxa and their metabolic pathways studied using high-throughput metagenomics sequencing analysis. [ 13C]-labelled Metagenome-Assembled Genome closely related to the family Beijerinckiaceae may represent a new methylotroph family of Alphaproteobacteria, which is found in metagenome databases of forest soils samples worldwide. Gene markers of the only known pathway for aerobic CH3 Cl degradation, via the methyltransferase system encoded by the CH3 Cl utilisation genes (cmu), were undetected in the DNA-SIP metagenome data, suggesting that biological CH3 Cl sink in this deciduous forest soil operates by a cmu-independent metabolism.

Methylocystis silviterrae sp.nov., a high-affinity methanotrophic bacterium isolated from the boreal forest soil

A novel species is proposed for a high-affinity methanotrophic representative of the genus Methylocystis . Strain FST was isolated from a weakly acidic (pH 5.3) mixed forest soil of the southern Moscow area. Cells of FST are aerobic, Gram-negative, non-motile, curved coccoids or short rods that contain an intracytoplasmic membrane system typical of type-II methanotrophs. Only methane and methanol are used as carbon sources. FST grew at a temperature range of 4–37 °C (optimum 25–30 °C) and a pH range of 4.5 to 7.5 (optimum pH 6.0–6.5). The major fatty acids were C18 : 1ω8c, C18 : 1ω7c and C18 : 0; the major quinone as Q-8. FST displays 16S rRNA gene sequences similarity to other taxonomically recognized members of the genus Methylocystis, with Methylocystis hirsuta CSC1T (99.6 % similarity) and Methylocystis rosea SV97T (99.3 % similarity) as its closest relatives. The genome comprises 3.85 Mbp and has a DNA G+C content of 62.6 mol%. Genomic analyses and DNA–DNA relatedness with genome-sequenced members of the genus Methylocystis demonstrated that FST could be separated from its closest relatives. FST possesses two particulate methane monooxygenases (pMMO): low-affinity pMMO1 and high-affinity pMMO2. In laboratory experiments, it was demonstrated that FST might oxidize methane at atmospheric concentration. The genome contained various genes for nitrogen fixation, polyhydroxybutyrate synthesis, antibiotic resistance and detoxification of arsenic, cyanide and mercury. On the basis of genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species, Methylocystis silviterrae sp. nov. The type strain is FST (=KCTC 82935T=VKM B-3535T).