Microbial diversity plays an important role in the decomposition of soil organic matter. However, the pattern and drivers of the relationship between microbial diversity and decomposition remain unclear. In this study, we followed the decomposition of organic matter in soils where microbial diversity was experimentally manipulated. To produce a gradient of microbial diversity, we used soil samples at two sites of the same chronosequence after brown coal mining in Sokolov, Czech Republic. Soils were X-ray sterilized and inoculated by two densities of inoculum from both soils and planted with seeds of six local plant species. This created two soils each with four levels of microbial diversity characterized by next-generation sequencing. These eight soils were supplied, or not, by litter of the bushgrass Calamagrostis epigejos, and microbial respiration was measured to assess the rate of decomposition. A strong positive correlation was found between microbial diversity and decomposition of organic matter per gram of carbon in soil, which suggests that microbial diversity supports decomposition if the microbial community is limited by available carbon. In contrast, microbial respiration per gram of soil negatively correlated with bacterial diversity and positively with fungal biomass, suggesting that in the absence of a carbon limitation, decomposition rate is controlled by the amount of fungal biomass. Soils with the addition of grass litter showed a priming effect in the initial stage of decomposition compared to the samples without the addition of litter. Thus, the relationship between microbial diversity and the rate of decomposition may be complex and context dependent.

• Keywords
• carbon availability, decomposition of soil organic matter, fungal biomass, leaf litter, microbial biomass, microbial diversity,
• Publication type
• Journal Article MeSH

Soil microorganisms are diverse, although they share functions during the decomposition of organic matter. Thus, preferences for soil conditions and litter quality were explored to understand their niche partitioning. A 1-year-long litterbag transplant experiment evaluated how soil physicochemical traits of contrasting sites combined with chemically distinct litters of sedge (S), milkvetch (M) from a grassland, and beech (B) from forest site decomposition. Litter was assessed by mass loss; C, N, and P contents; and low-molecular-weight compounds. Decomposition was described by the succession of fungi, Actinobacteria, Alphaproteobacteria, and Firmicutes; bacterial diversity; and extracellular enzyme activities. The M litter decomposed faster at the nutrient-poor forest site, where the extracellular enzymes were more active, but microbial decomposers were not more abundant. Actinobacteria abundance was affected by site, while Firmicutes and fungi by litter type and Alphaproteobacteria by both factors. Actinobacteria were characterized as late-stage substrate generalists, while fungi were recognized as substrate specialists and site generalists, particularly in the grassland. Overall, soil conditions determined the decomposition rates in the grassland and forest, but successional patterns of the main decomposers (fungi and Actinobacteria) were determined by litter type. These results suggest that shifts in vegetation mostly affect microbial decomposer community composition.IMPORTANCE Anthropogenic disturbance may cause shifts in vegetation and alter the litter input. We studied the decomposition of different litter types under soil conditions of a nutrient-rich grassland and nutrient-poor forest to identify factors responsible for changes in the community structure and succession of microbial decomposers. This will help to predict the consequences of induced changes on the abundance and activity of microbial decomposers and recognize if the decomposition process and resulting quality and quantity of soil organic matter will be affected at various sites.

• Keywords
• enzyme activities, forest, grassland, organic matter, succession,
• MeSH
• Bacteria classification   metabolism   MeSH
• Biodiversity MeSH
• Ecosystem MeSH
• Fungi classification   metabolism   MeSH
• Forests MeSH
• Microbiota * MeSH
• Grassland MeSH
• Soil chemistry   MeSH
• Soil Microbiology * MeSH
• RNA, Ribosomal, 16S MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Soil MeSH
• RNA, Ribosomal, 16S MeSH

Two long-term contaminated soils differing in contents of Pb, Zn, As, Cd were compared in a microcosm experiment for changes in microbial community structure and respiration after various treatments. We observed that the extent of long-term contamination (over 200 years) by toxic elements did not change the total numbers and diversity of bacteria but influenced their community composition. Namely, numbers of Actinobacteria determined by phylum specific qPCR increased and also the proportion of Actinobacteria and Chloroflexi increased in Illumina sequence libraries in the more contaminated soil. In the experiment, secondary disturbance by supplemented cadmium (doses from double to 100-fold the concentration in the original soil) and organic substrates (cellobiose or straw) increased bacterial diversity in the less contaminated soil and decreased it in the more contaminated soil. Respiration in the experiment was higher in the more contaminated soil in all treatments and correlated with bacterial numbers. Considering the most significant changes in bacterial community, it seemed that particularly Actinobacteria withstand contamination by toxic elements. The results proved higher resistance to secondary disturbance in terms of both, respiration and bacterial community structure in the less contaminated soil.

• Keywords
• actinobacteria, cellobiose, diversity, respiration, straw,
• Publication type
• Journal Article MeSH

BACKGROUND: Distribution and evolutionary history of resistance genes in environmental actinobacteria provide information on intensity of antibiosis and evolution of specific secondary metabolic pathways at a given site. To this day, actinobacteria producing biologically active compounds were isolated mostly from soil but only a limited range of soil environments were commonly sampled. Consequently, soil remains an unexplored environment in search for novel producers and related evolutionary questions. RESULTS: Ninety actinobacteria strains isolated at contrasting soil sites were characterized phylogenetically by 16S rRNA gene, for presence of erm and ABC transporter resistance genes and antibiotic production. An analogous analysis was performed in silico with 246 and 31 strains from Integrated Microbial Genomes (JGI_IMG) database selected by the presence of ABC transporter genes and erm genes, respectively. In the isolates, distances of erm gene sequences were significantly correlated to phylogenetic distances based on 16S rRNA genes, while ABC transporter gene distances were not. The phylogenetic distance of isolates was significantly correlated to soil pH and organic matter content of isolation sites. In the analysis of JGI_IMG datasets the correlation between phylogeny of resistance genes and the strain phylogeny based on 16S rRNA genes or five housekeeping genes was observed for both the erm genes and ABC transporter genes in both actinobacteria and streptomycetes. However, in the analysis of sequences from genomes where both resistance genes occurred together the correlation was observed for both ABC transporter and erm genes in actinobacteria but in streptomycetes only in the erm gene. CONCLUSIONS: The type of erm resistance gene sequences was influenced by linkage to 16S rRNA gene sequences and site characteristics. The phylogeny of ABC transporter gene was correlated to 16S rRNA genes mainly above the genus level. The results support the concept of new specific secondary metabolite scaffolds occurring more likely in taxonomically distant producers but suggest that the antibiotic selection of gene pools is also influenced by site conditions.

• MeSH
• ATP-Binding Cassette Transporters genetics   MeSH
• Actinobacteria classification   drug effects   genetics   isolation & purification   MeSH
• Anti-Bacterial Agents biosynthesis   MeSH
• Drug Resistance, Bacterial * MeSH
• Phylogeny * MeSH
• Genes, rRNA MeSH
• Methyltransferases genetics   MeSH
• Molecular Sequence Data MeSH
• Soil Microbiology MeSH
• DNA, Ribosomal chemistry   genetics   MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Sequence Analysis, DNA MeSH
• Cluster Analysis MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• ATP-Binding Cassette Transporters MeSH
• Anti-Bacterial Agents MeSH
• Methyltransferases MeSH
• DNA, Ribosomal MeSH
• RNA, Ribosomal, 16S MeSH
• rRNA (adenosine-O-2'-)methyltransferase MeSH Browser

BACKGROUND: Bacteria are associated with the gut, fat bodies and reproductive organs of stored product mites (Acari: Astigmata). The mites are pests due to the production of allergens. Addition of antibiotics to diets can help to characterize the association between mites and bacteria. METHODOLOGY AND PRINCIPAL FINDINGS: Ampicillin, neomycin and streptomycin were added to the diets of mites and the effects on mite population growth (Acarus siro, Lepidoglyphus destructor and Tyrophagus putrescentiae) and associated bacterial community structure were assessed. Mites were treated by antibiotic supplementation (1 mg g(-1) of diet) for 21 days and numbers of mites and bacterial communities were analyzed and compared to the untreated control. Bacterial quantities, determined by real-time PCR, significantly decreased in antibiotic treated specimens from 5 to 30 times in A. siro and T. putrescentiae, while no decline was observed in L. destructor. Streptomycin treatment eliminated Bartonella-like bacteria in the both A. siro and T. putrescentiae and Cardinium in T. putrescentiae. Solitalea-like bacteria proportion increased in the communities of neomycin and streptomycin treated A. siro specimens. Kocuria proportion increased in the bacterial communities of ampicillin and streptomycin treated A. siro and neomycin and streptomycin treated L. destructor. CONCLUSIONS/SIGNIFICANCE: The work demonstrated the changes of mite associated bacterial community under antibiotic pressure in pests of medical importance. Pre-treatment of mites by 1 mg g(-1) antibiotic diets improved mite fitness as indicated accelerated population growth of A. siro pretreated streptomycin and neomycin and L. destructor pretreated by neomycin. All tested antibiotics supplemented to diets caused the decrease of mite growth rate in comparison to the control diet.

• MeSH
• Acaridae drug effects   growth & development   microbiology   MeSH
• Ampicillin pharmacology   MeSH
• Anti-Bacterial Agents pharmacology   MeSH
• Bacteria genetics   MeSH
• Population Density MeSH
• Microbial Consortia drug effects   MeSH
• Neomycin pharmacology   MeSH
• RNA, Ribosomal, 16S MeSH
• Streptomycin pharmacology   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Ampicillin MeSH
• Anti-Bacterial Agents MeSH
• Neomycin MeSH
• RNA, Ribosomal, 16S MeSH
• Streptomycin MeSH