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Ammonia-oxidizing thaumarcheota ( AOA) and ammonia-oxidizing bacteria ( AOB) differentially influence soil and atmospheric chemistry, but soil properties that control their distributions are poorly understood. In this study, the ammonia monooxygenase gene ( amoA) was used to identify and quantify presumptive AOA and AOB and relate their distributions to soil properties in two experimental fields planted with different varieties of switchgrass ( P anicum virgatum), a potential bioenergy feedstock. Differences in ammonia oxidizer diversity were associated primarily with soil properties of the two field sites, with pH displaying significant correlations with both AOA and AOB population structure. Percent nitrogen (%N), carbon to nitrogen ratios (C : N), and pH were also correlated with shifts nitrifier population structure. N itrosotalea-like and N itrosospira cluster II populations were more highly represented in acidic soils, whereas populations affiliated with N itrososphaera and N itrosospira cluster 3 A.1 were relatively more abundant in alkaline soils. AOA were the dominant functional group in all plots based on quantitative polymerase chain reaction and high-throughput sequencing analyses. These data suggest that AOA contribute significantly to nitrification rates in carbon and nitrogen rich soils influenced by perennial grasses. [ABSTRACT FROM AUTHOR]

Deep lakes are of specific interest in the study of archaeal assemblages as chemical stratification in the water column allows niche differentiation and distinct community structure. Active archaeal community and potential nitrifiers were investigated monthly over 1 year by pyrosequencing 16 S rRNA transcripts and genes, and by quantification of archaeal amoA genes in two deep lakes. Our results showed that the active archaeal community patterns of spatial and temporal distribution were different between these lakes. The meromictic lake characterized by a stable redox gradient but variability in nutrient concentrations exhibited large temporal rearrangements of the dominant euryarchaeal phylotypes, suggesting a variety of ecological niches and dynamic archaeal communities in the hypolimnion of this lake. Conversely, T haumarchaeota Marine Group I (MGI) largely dominated in the second lake where deeper water layers exhibited only short periods of complete anoxia and constant low ammonia concentrations. Investigations conducted on archaeal amoA transcripts abundance suggested that not all lacustrine T haumarchaeota conduct the process of nitrification. A high number of 16 S rRNA transcripts associated to crenarchaeal group C3 or the Miscellaneous Euryarchaeotic Group indicates the potential for these uncharacterized groups to contribute to nutrient cycling in lakes. [ABSTRACT FROM AUTHOR]

The existence of microbial communities and the complex interactions that govern their dynamics have received considerable attention in recent years. Advances in genomic sequencing technologies have greatly enhanced our understanding of 'what is there'. However, the question as to 'what are they doing' remains less well defined. The continual development of the genomic and metagenomic sequence databases provides an exciting opportunity to interrogate the distribution and prevalence of key microbial systems across a diverse set of ecosystems. The widely distributed type VI secretion system ( T6SS) has been shown to play a significant role in bacterial-bacterial and bacterial-host interactions. While several T6SS effectors have been shown to target the cell wall and membrane of competing cells, little is known about the roles these proteins play in different ecosystems. Therefore, the prevalence of a key T6SS effector superfamily known as type six lipase effectors ( Tle) was studied in over 2000 metagenomic datasets representing diverse ecosystems and host niches. Increased Tle representation in environmental categories strongly supports the hypothesis of niche specialization and suggests that these effectors may play important niche-specific roles. [ABSTRACT FROM AUTHOR]

The discovery of denitrifying anaerobic methane oxidation with nitrite as electron acceptor mediated by ' C andidatus Methylomirabilis oxyfera' connected the biogeochemical carbon and nitrogen cycle in a new way. However, it is important to have a comprehensive understanding about the distribution of M . oxyfera-like bacteria in the terrestrial realm, especially the wetland ecosystems that are known as the largest natural source of atmospheric methane. Here, our molecular evidence demonstrated that a wide geographical distribution of M . oxyfera-like bacteria at oxic/anoxic interfaces of various wetlands ( n = 91) over the Chinese territory. Intriguingly, the M . oxyfera-like bacteria were detected in some extreme environments, indicating that M . oxyfera-like bacteria occupied a wide range of habitats. Quantitative polymerase chain reaction estimated that the abundance of M . oxyfera-like bacteria ranged from 2.2 × 103 to 2.3 × 107 copies g−1 dry soil, and up to around 0.62% of the total number of bacteria. Moreover, the M . oxyfera-like bacteria showed high biodiversity in wetland ecosystems based on the analysis of 462 pmoA and 287 16S rRNA gene sequences. The current study revealed the widespread distribution and biogeography of M . oxyfera-like bacteria in the terrestrial system. [ABSTRACT FROM AUTHOR]