Dataset Information

Distribution and Diversity of Comammox Nitrospira in Coastal Wetlands of China.

ABSTRACT: Complete ammonia oxidizers (comammox), able to individually oxidize ammonia to nitrate, are considered to play a significant role in the global nitrogen cycle. However, the distribution of comammox Nitrospira in estuarine tidal flat wetland and the environmental drivers affecting their abundance and diversity remain unknown. Here, we present a large-scale investigation on the geographical distribution of comammox Nitrospira along the estuarine tidal flat wetlands of China, where comammox Nitrospira were successfully detected in 9 of the 16 sampling sites. The abundance of comammox Nitrospira ranged from 5.19 × 10³ to 8.33 × 10⁴ copies/g, 2.21 to 5.44-folds lower than canonical ammonia oxidizers: ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Phylogenetic analysis based on the alpha subunit of the ammonia monooxygenase encoding gene (amoA) revealed that comammox Nitrospira Clade A, mainly originating from upstream river inputs, accounts for more than 80% of the detected comammox Nitrospira, whereas comammox Nitrospira clade B were rarely detected. Comammox Nitrospira abundance and dominant comammox Nitrospira OTUs varied within the estuarine samples, showing a geographical pattern. Salinity and pH were the most important environmental drivers affecting the distribution of comammox Nitrospira in estuarine tidal flat wetlands. The abundance of comammox Nitrospira was further negatively correlated with high ammonia and nitrite concentrations. Altogether, this study revealed the existence, abundance and distribution of comammox Nitrospira and the driving environmental factors in estuarine ecosystems, thus providing insights into the ecological niches of this recently discovered nitrifying consortium and their contributions to nitrification in global estuarine environments.

SUBMITTER: Sun D

PROVIDER: S-EPMC7573150 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Complete ammonia oxidizers (comammox Nitrospira) are ubiquitous in coastal wetland sediments and play an important role in nitrification. Our study examined the impact of habitat modifications on comammox Nitrospira communities in coastal wetland sediments across tropical and subtropical regions of southeastern China. Samples were collected from 21 coastal wetlands in five provinces where native mudflats were invaded by Spartina alterniflora and subsequently converted to aquaculture ponds. The results showed that comammox Nitrospira abundances were mainly influenced by sediment grain size rather than by habitat modifications. Compared to S. alterniflora marshes and native mudflats, aquaculture pond sediments had lower comammox Nitrospira diversity, lower clade A.1 abundance, and higher clade A.2 abundance. Sulfate concentration was the most important factor controlling the diversity of comammox Nitrospira. The response of comammox Nitrospira community to habitat change varied significantly by location, and environmental variables accounted for only 11.2% of the variations in community structure across all sites. In all three habitat types, dispersal limitation largely controlled the comammox Nitrospira community assembly process, indicating the stochastic nature of these sediment communities in coastal wetlands. IMPORTANCE Comammox Nitrospira have recently gained attention for their potential role in nitrification and nitrous oxide (N2O) emissions in soil and sediment. However, their distribution and assembly in impacted coastal wetland are poorly understood, particularly on a large spatial scale. Our study provides novel evidence that the effects of habitat modification on comammox Nitrospira communities are dependent on the location of the wetland. We also found that the assembly of comammox Nitrospira communities in coastal wetlands was mainly governed by stochastic processes. Nevertheless, sediment grain size and sulfate concentration were identified as key variables affecting comammox Nitrospira abundance and diversity in coastal sediments. These findings are significant as they advance our understanding of the environmental adaptation of comammox Nitrospira and how future landscape modifications may impact their abundance and diversity in coastal wetlands.

Project description:Microbes commonly exist in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species interaction and evolution has increased during the last decades, but most studies of evolutionary dynamics are based on single species in isolation or in experimental systems composed of few interacting species. Here, we use the microbial ecosystem found in groundwater-fed sand filter as a model to avoid this limitation. In these open systems, diverse microbial communities experience relatively stable conditions, and the coupling between chemical and biological processes is generally well defined. Metagenomic analysis of 12 sand filters communities revealed systematic co-occurrence of at least five comammox Nitrospira species, likely promoted by low ammonium concentrations. These Nitrospira species showed intrapopulation sequence diversity, although possible clonal expansion was detected in a few abundant local comammox populations. Nitrospira species showed low homologous recombination and strong purifying selection, the latter process being especially strong in genes essential in energy metabolism. Positive selection was detected for genes related to resistance to foreign DNA and phages. We found that, compared to other habitats, groundwater-fed sand filters impose strong purifying selection and low recombination on comammox Nitrospira populations. These results suggest that evolutionary processes are more affected by habitat type than by species identity. Together, this study improves our understanding of species interaction and evolution in complex microbial communities and sheds light on the environmental dependency of evolutionary processes. IMPORTANCE Microbial species interact with each other and their environment (ecological processes) and undergo changes in their genomic repertoire over time (evolutionary processes). How these two classes of processes interact is largely unknown, especially for complex communities, as most studies of microbial evolutionary dynamics consider single species in isolation or a few interacting species in simplified experimental systems. In this study, these limitations are circumvented by examining the microbial communities found in stable and well-described groundwater-fed sand filters. Combining metagenomics and strain-level analyses, we identified the microbial interactions and evolutionary processes affecting comammox Nitrospira, a recently discovered bacterial type capable of performing the whole nitrification process. We found that abundant and co-occurrent Nitrospira populations in groundwater-fed sand filters are characterized by low recombination and strong purifying selection. In addition, by comparing these observations with those obtained from Nitrospira species inhabiting other environments, we revealed that evolutionary processes are more affected by habitat type than by species identity.

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Distribution and Diversity of Comammox Nitrospira in Coastal Wetlands of China.

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