Genome, genetic evolution, and environmental adaptation mechanisms of Schizophyllum commune in deep subseafloor coal-bearing sediments

Li, Xuan; Huang, Xin; Chu, Chia‐Yu; Xu, Hui; Wang, Long; Xue, Yarong; Muhammad, Zain Ul Arifeen; Inagaki, Fumio; Liu, Changhong

doi:10.1016/j.isci.2022.104417

“…The absence of archaeal and bacterial contaminants was further confirmed by PCR amplification of 16S rRNA and methyl coenzyme M reductase ( mcrA ) genes in the fungal mycelia and culture filtrate (see Fig. S1A in the supplemental material), as well as whole-genome sequencing, which did not yield any recognizable prokaryotic gene sequences ( 26 ). In addition, confocal laser scanning microscope (CLSM) observation showed that, except for some general cell internal autofluorescence, no autofluorescence signal (Fig.…”

Section: Resultsmentioning

confidence: 96%

Methane Production by Facultative Anaerobic Wood-Rot Fungi via a New Halomethane-Dependent Pathway

Huang

¹

,

Li

²

,

Xue

³

et al. 2022

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“…and the other five terrestrial strains (225DK, 227DK, MF, Hom2-8, and 207) were obtained from NCBI and JGI database. Details of the habitat and culture conditions of S. commune strains have been described previously ( Liu et al, 2022 ). All the fungal strains were maintained on potato dextrose agar (PDA) at 30°C.…”

Section: Methodsmentioning

confidence: 99%

“…The genome resequencing and variant detection for S. commune strains were carried out according to our previous methods ( Liu et al, 2022 ). Briefly, the genome DNA of S. commune strains was extracted and fragmented to generate an approximately 300 bp library insert size and sequenced on an Illumina HiSeq 2500 platform at BGI Genomic (Shenzhen, China).…”

Section: Methodsmentioning

confidence: 99%

“…and the other five terrestrial strains (225DK, 227DK, MF, Hom2-8, and 207) were obtained from NCBI and JGI database. Details of the habitat and culture conditions of S. commune strains have been described previously (Liu et al, 2022). All the fungal strains were maintained on potato dextrose agar (PDA) at 30 • C. For DNA and RNA isolations, the fresh mycelia of S. commune were inoculated into a 250-ml conical flask containing 150 ml PD (200 g/L potato, 20 g/L glucose) and incubated in a shaking chamber at 30 • C, 200 rpm for 7 days.…”

Section: Strains and Culture Conditionsmentioning

confidence: 99%

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Genome-wide characterization of laccase gene family in Schizophyllum commune 20R-7-F01, isolated from deep sediment 2 km below the seafloor

Li

¹

,

Arifeen²,

Xue³

et al. 2022

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Laccases are ligninolytic enzymes that play a crucial role in various biological processes of filamentous fungi, including fruiting-body formation and lignin degradation. Lignin degradation is a complex process and its degradation in Schizophyllum commune is greatly affected by the availability of oxygen. Here, a total of six putative laccase genes (ScLAC) were identified from the S. commune 20R-7-F01 genome. These genes, which include three typical Cu-oxidase domains, can be classified into three groups based on phylogenetic analysis. ScLAC showed distinct intron-exon structures and conserved motifs, suggesting the conservation and diversity of ScLAC in gene structures. Additionally, the number and type of cis-acting elements, such as substrate utilization-, stress-, cell division- and transcription activation-related cis-elements, varied between ScLAC genes, suggesting that the transcription of laccase genes in S. commune 20R-7-F01 could be induced by different substrates, stresses, or other factors. The SNP analysis of resequencing data demonstrated that the ScLAC of S. commune inhabiting deep subseafloor sediments were significantly different from those of S. commune inhabiting terrestrial environments. Similarly, the large variation of conserved motifs number and arrangement of laccase between subseafloor and terrestrial strains indicated that ScLAC had a diverse structure. The expression of ScLAC5 and ScLAC6 genes was significantly up-regulated in lignin/lignite medium, suggesting that these two laccase genes might be involved in fungal utilization and degradation of lignite and lignin under anaerobic conditions. These findings might help in understanding the function of laccase in white-rot fungi and could provide a scientific basis for further exploring the relationship between the LAC family and anaerobic degradation of lignin by S. commune.

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“…For example, the r / m values from the genomes of subseafloor bacteria Thalassospira spp. ( 8 ) and fungi Schizophyllum commune ( 9 ), which were isolated from million-year-old sediments from different sites, ranged between 0.05 and 0.07, up to three orders of magnitude lower than that of their terrestrial type strains. The findings of extremely low r / m values for subseafloor life indicate that a lack of homologous recombination in genomic evolution may be a general feature of subseafloor microbial evolution in the deep sedimentary biosphere.…”

mentioning

confidence: 99%