Understanding the influence of vegetation types on soil particle-size distribution (PSD) is essential to evaluate the effects of sediment control by vegetation restoration. In this work, we studied the effects of different vegetation types, including bare land, meadow, shrub and forest on soil PSD in Jiangjiagou gully, Yunnan province, China. A total of 60 soil samples were collected and analyzed for soil particle size distribution using the laser diffraction method. Fractal theory was used to calculate multifractal parameters. The volume fraction of silt particles in shrub and forest is significantly higher than that in bare land, meadow, whereas the total volume fraction of sand particles in bare land and meadow exceed that in shrub and forest. The soil particle size distribution along soil layers has no significant difference in each vegetation type. The volumetric fractal dimension is significantly higher in forest and shrub than in bare land and grassland, but there is no significant difference between forest and shrub. In addition, soil erosion resistance exhibits significant differences of forest > shrub > grassland > bare land. Multifractal parameters are highest in bare land except for multifractal spectrum values ( f (α max ) and f (α min )) and the maximum value of singularity index (α min ). All generalized dimensions spectra curves of the PSD are sigmoidal, whereas the singular spectrum function shows an asymmetric upward convex curve. Furthermore, soil erosion resistance has significant relationships with multifractal parameters. Our results suggest that multifractal parameters of the soil PSD can predict its anti-ability to erosion. This study also provides an important insight for the evaluation of soil structure improvement and the effects of erosion control by vegetation restoration in dry-hot valley areas.
Chemolithoautotrophic manganese oxidation has long been theorized but only recently demonstrated in a bacterial coculture. The majority member of the coculture, "Candidatus Manganitrophus noduliformans," is a distinct but not yet isolated lineage in the phylum Nitrospirota (Nitrospirae). Here, we established two additional MnCO3-oxidizing cultures using inocula from Santa Barbara (California) and Boetsap (South Africa). Both cultures were dominated by strains of a new species, designated "Candidatus Manganitrophus morganii." The next most abundant members differed in the available cultures, suggesting that while "Ca. Manganitrophus" species have not been isolated in pure culture, they may not require a specific syntrophic relationship with another species. Phylogeny of cultivated "Ca. Manganitrophus" and related metagenome-assembled genomes revealed a coherent taxonomic family, "Candidatus Manganitrophaceae," from both freshwater and marine environments and distributed globally. Comparative genomic analyses support this family being Mn(II)-oxidizing chemolithoautotrophs. Among the 895 shared genes were a subset of those hypothesized for Mn(II) oxidation (Cyc2 and PCC_1) and oxygen reduction (TO_1 and TO_2) that could facilitate Mn(II) lithotrophy. An unusual, plausibly reverse complex 1 containing 2 additional pumping subunits was also shared by the family, as were genes for the reverse tricarboxylic acid carbon fixation cycle, which could enable Mn(II) autotrophy. All members of the family lacked genes for nitrification found in Nitrospira species. The results suggest that "Ca. Manganitrophaceae" share a core set of candidate genes for the newly discovered manganese-dependent chemolithoautotrophic lifestyle and likely have a broad, global distribution. IMPORTANCE Manganese (Mn) is an abundant redox-active metal that cycles in many of Earth's biomes. While diverse bacteria and archaea have been demonstrated to respire Mn(III/IV), only recently have bacteria been implicated in Mn(II) oxidation-dependent growth. Here, two new Mn(II)-oxidizing enrichment cultures originating from two continents and hemispheres were examined. By comparing the community composition of the enrichments and performing phylogenomic analysis on the abundant Nitrospirota therein, new insights are gleaned on cell interactions, taxonomy, and machineries that may underlie Mn(II)-based lithotrophy and autotrophy.
Abstract The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota , none of which have been isolated in pure culture. Here we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features which separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well-distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.
The oxidation of methane with sulfate is an important microbial metabolism in the global carbon cycle. In marine methane seeps, this process is mediated by consortia of anaerobic methanotrophic archaea (ANME) that live in syntrophy with sulfate-reducing bacteria (SRB). The underlying interdependencies within this uncultured symbiotic partnership are poorly understood. We used a combination of rate measurements and single-cell stable isotope probing to demonstrate that ANME in deep-sea sediments can be catabolically and anabolically decoupled from their syntrophic SRB partners using soluble artificial oxidants. The ANME still sustain high rates of methane oxidation in the absence of sulfate as the terminal oxidant, lending support to the hypothesis that interspecies extracellular electron transfer is the syntrophic mechanism for the anaerobic oxidation of methane.
Figure 2 of manuscript "Comparative genomics and proteomic analysis of assimilatory sulfate reduction pathways in anaerobic methanotrophic archaea" Files included:Fig2_cysN_ef_clustalo_alignment.faa - ClustalO alignment of protein sequencesFig2_cysN_ef_clustalo_alignment_filtered_for_tree.faa - Filtered protein sequences (416 amino acids) used for phylogeneticsFig2_cysN_ef_clustalo_tree.png - Final Bayesian Phylogeny of CysN and Elongation FactorFig2_cysD_clustalo_alignment.faa - ClustalO alignment of protein sequencesFig2_cysD_clustalo_alignment_filtered_for_tree.faa - Filtered protein sequences (416 amino acids) used for phylogeneticsFig2_cysD_clustalo_tree.png - Final Bayesian Phylogeny of CysN and Elongation Factor Figure 2. Phylogeny of heterodimeric ATP sulfurylase subunits (CysDN). (a) Bayesian phylogeny of 416 amino acid residues of sulfate adenylyltransferase subunit 1 (CysN) and elongation factor 1 alpha (EF-1A) or elongation factor thermo unstable (EF-Tu) proteins. CysN, in green, formed a separate phylogenetic cluster from the homologous EF-1A and EF-Tu in blue. ANME proteins are bolded in red. The phylogenetic analysis distinguished CysN from their homologous elongation factor in ANME. (b) Bayesian phylogeny of 270 amino acid residues of sulfate adenylyltransferase subunit 2 (CysD) in green. They are found in ANME genomes next to CysN confirming that they are the heterodimeric ATP sulfurylase subunits. Asterisks (*) indicate proteins that have been studied biochemically or structurally (Andersen et al., 2000; Kobayashi et al., 2010; Liu et al., 1994; Mougous et al., 2006; Schmeing et al., 2009; Thirup et al., 2015; Vitagliano et al., 2001). Protein accession numbers from the NCBI database or gene IDs from the IMG database are shown in parentheses. Black dots on the branches represent Bayesian posterior probability values greater than 90%, and scale bar indicates the number of amino acid substitutions per site.
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