The Amazon rainforest, the largest equatorial forest in the world, is being cleared for pasture and agricultural use at alarming rates. Tropical deforestation is known to cause alterations in microbial communities at taxonomic and phylogenetic levels, but it is unclear whether microbial functional groups are altered. We asked whether free-living nitrogen-fixing microorganisms (diazotrophs) respond to deforestation in the Amazon rainforest, using analysis of the marker gene nifH. Clone libraries were generated from soil samples collected from a primary forest, a 5-year-old pasture originally converted from primary forest, and a secondary forest established after pasture abandonment. Although diazotroph richness did not significantly change among the three plots, diazotroph community composition was altered with forest-to-pasture conversion, and phylogenetic similarity was higher among pasture communities than among those in forests. There was also 10-fold increase in nifH gene abundance following conversion from primary forest to pasture. Three environmental factors were associated with the observed changes: soil acidity, total N concentration, and C/N ratio. Our results suggest a partial restoration to initial levels of abundance and community structure of diazotrophs following pasture abandonment, with primary and secondary forests sharing similar communities. We postulate that the response of diazotrophs to land use change is a direct consequence of changes in plant communities, particularly the higher N demand of pasture plant communities for supporting aboveground plant growth.

Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem’s decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change.

A significant proportion of oral bacteria are unable to undergo cultivation by existing techniques. In this regard, the microbiota from root canals still requires complementary characterization. The present study aimed at the identification of bacteria by sequence analysis of 16S rDNA clone libraries from seven endodontically infected teeth. Samples were collected from the root canals, subjected to the PCR with universal 16S rDNA primers, cloned and partially sequenced. Clones were clustered into groups of closely related sequences (phylotypes) and identification to the species level was performed by comparative analysis with the GenBank, EMBL and DDBJ databases, according to a 98 % minimum identity. All samples were positive for bacteria and the number of phylotypes detected per subject varied from two to 14. The majority of taxa (65?2 %) belonged to the phylum Firmicutes of the Gram-positive bacteria, followed by Proteobacteria (10?9 %), Spirochaetes (4?3 %), Bacteroidetes (6?5 %), Actinobacteria (2?2 %) and Deferribacteres (2?2 %). A total of 46 distinct taxonomic units was identified. Four clones with low similarity to sequences previously deposited in the databases were sequenced to nearly full extent and were classified taxonomically as novel representatives of the order Clostridiales, including a putative novel species of Mogibacterium. The identification of novel phylotypes associated with endodontic infections suggests that the endodontium may still harbour a relevant proportion of uncharacterized taxa. INTRODUCTIONAlthough more than 150 species of bacteria have been identified in infected root canals, only a restricted number can be found simultaneously in the same tooth and a considerable variation of species is expected when analysing distinct clinical conditions, individuals or populations (Sundqvist, 1976;Molander et al., 1998;Baumgartner et al., 2004). Cultivation studies have shown a predominance of facultative and strict anaerobes in the endodontium, including representatives of Eubacterium, Fusobacterium, Peptococcus, Peptostreptococcus, Porphyromonas, Prevotella and (Sundqvist, 1992b;Le Goff et al., 1997). Bacteria inside the canal are the major cause of periapical pathologies (Kakehashi et al., 1965) and, if not adequately treated, can give rise to dentoalveolar abscess, a condition that has ability to initiate morbidity, life-threatening illness (Walsh, 1997), and to predispose to transient bacteraemia during therapy (Savarrio et al., 2005). Previous reports suggested that endodontic bacteria might be involved in extra-oral complications, such as chronic maxillary sinusitis (Melen et al., 1986), orbital cellulitis (Ngeow, 1999), infective endocarditis (Bate et al., 2000), rheumatoid arthritis (Breebaart et al., 2002) and brain abscess (Henig et al., 1978). In this regard, substantial understanding of the endodontic microbiota is an important requirement for both oral and medical microbiologists. StreptococcusWhile it is common knowledge that the development of efficient treatment strategies ...

We evaluated the bacterial and archaeal community dynamics and assembly in soils under forest, grassland and no-till cropping, using a high-throughput shotgun metagenomics approach. No significant alterations in alpha diversity were observed among different land uses, but beta diversity in grassland was lower than that observed in forest and no-till soils. Grassland communities showed assembly that predominantly followed the neutral model, i.e. high homogenizing selection with moderate dispersion, leading to biotic homogenization. Both no-till and forest soil communities were found to have assembly that predominantly followed a niche model, i.e. low rates of dispersal and weak homogenizing selection, resulting in maintenance of higher beta diversity relative to grasslands, indicating niche specialization or variable selection. Taken together, our results indicate that the patterns of assembly and their governing processes are dependent on the land use employed after deforestation, with consequences for taxa turnover and microbial functional potential.

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Deforestation in the Brazilian Amazon occurs at an alarming rate, which has broad effects on global greenhouse gas emissions, carbon storage, and biogeochemical cycles. In this study, soil metagenomes and metagenome-assembled genomes (MAGs) were analyzed for alterations to microbial community composition, functional groups, and putative physiology as it related to land-use change and tropical soil. A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. Amazon Acidobacteria subdivision 3, Melainabacteria, Microgenomates, and Parcubacteria were found exclusively in pasture soil samples, while Candidatus Rokubacteria was predominant in the adjacent rainforest soil. These shifts in relative abundance between land-use types were supported by the different putative physiologies and life strategies employed by the taxa. This research provides unique biological insights into candidate phyla in tropical soil and how deforestation may impact the carbon cycle and affect climate change.

Co-occurrence networks allow for the identification of potential associations among species, which may be important for understanding community assembly and ecosystem functions. We employed this strategy to examine prokaryotic co-occurrence patterns in the Amazon soils and the response of these patterns to land use change to pasture, with the hypothesis that altered microbial composition due to deforestation will mirror the co-occurrence patterns across prokaryotic taxa. In this study, we calculated Spearman correlations between operational taxonomic units (OTUs) as determined by 16S rRNA gene sequencing, and only robust correlations were considered for network construction (−0.80 ≥ P ≥ 0.80, adjusted P < 0.01). The constructed network represents distinct forest and pasture components, with altered compositional and topological features. A comparative analysis between two representative modules of these contrasting ecosystems revealed novel information regarding changes to metabolic pathways related to nitrogen cycling. Our results showed that soil physicochemical properties such as temperature, C/N and H++Al3+ had a significant impact on prokaryotic communities, with alterations to network topologies. Taken together, changes in co-occurrence patterns and physicochemical properties may contribute to ecosystem processes including nitrification and denitrification, two important biogeochemical processes occurring in tropical forest systems.

Grazing and topography have drastic effects on plant communities and soil properties. These effects are thought to influence arbuscular mycorrhizal (AM) fungi. However, the simultaneous impacts of grazing pressure (sheep ha) and topography on plant and soil factors and their relationship to the production of extra-radical AM hyphae are not well understood. Our 10-year study assessed relationships between grazing, plant species richness, aboveground plant productivity, soil nutrients, edaphic properties, and AM hyphal length density (HLD) in different topographic areas (flat or sloped). We found HLD linearly declined with increasing grazing pressure (1.5-9.0 sheep ha) in sloped areas, but HLD was greatest at moderate grazing pressure (4.5 sheep ha) in flat areas. Structural equation modeling indicates grazing reduces HLD by altering soil nutrient dynamics in sloped areas, but non-linearly influences HLD through plant community and edaphic changes in flat areas. Our findings highlight how topography influences key plant and soil factors, thus regulating the effects of grazing pressure on extra-radical hyphal production of AM fungi in grasslands. Understanding how grazing and topography influence AM fungi in semi-arid grasslands is vital, as globally, severe human population pressure and increasing demand for food aggravate the grazing intensity in grasslands.