Comammox Nitrospira within the Yangtze River continuum: community, biogeography, and ecological drivers

Abstract The recent discovery of comammox Nitrospira as complete nitrifiers has fundamentally renewed perceptions of nitrogen cycling in natural and engineered systems, yet little is known about the environmental controls on these newly recognized bacteria. Based on improved phylogenetic resolution through successful assembly of ten novel genomes (71–96% completeness), we provided the first biogeographic patterns for planktonic and benthic comammox Nitrospira in the Yangtze River over a 6030 km continuum. Our study revealed the widespread distributions and relative abundance of comammox Nitrospira in this large freshwater system, constituting 30 and 46% of ammonia-oxidizing prokaryotes (AOPs) and displaying 30.4- and 17.9-fold greater abundances than canonical Nitrospira representatives in water and sediments, respectively. Comammox Nitrospira contributed more to nitrifier abundances (34–87% of AOPs) in typical oligotrophic environments with a higher pH and lower temperature, particularly in the plateau (clade B), mountain and foothill (clade A) areas of the upper reach. The dominant position of planktonic comammox Nitrospira was replaced by canonical Nitrospira sublineages I/II and ammonia-oxidizing bacteria from the plateau to downstream plain due to environmental selection, while the dissimilarity of benthic comammox Nitrospira was moderately associated with geographic distance. A substantial decrease (83%) in benthic comammox Nitrospira abundance occurred immediately downstream of the Three Gorges Dam, consistent with a similarly considerable decrease in overall sediment bacterial taxa. Together, this study highlights the previously unrecognized dominance of comammox Nitrospira in major river systems and underlines the importance of revisiting the distributions of and controls on nitrification processes within global freshwater environments.

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Biogeographic patterns of complete ammonia oxidizers (comammox) within the Yangtze River continuum

10.5194/egusphere-egu21-7121 ◽

2021 ◽

Author(s):

Shufeng Liu ◽

Haiying Wang ◽

Jinren Ni

Keyword(s):

Yangtze River ◽

Ammonia Oxidation ◽

Gene Clusters ◽

Anthropogenic Factors ◽

Ammonia Oxidizing Bacteria ◽

The Yangtze River ◽

Related Gene ◽

Biogeographic Patterns ◽

Environmental Selection ◽

Phylogenetic Resolution

The recent discovery of comammox Nitrospira performing complete ammonia oxidation to nitrate has fundamentally renewed the 120-year-held perspective of &#8220;two-step&#8221; nitrification. Rivers are known as the &#8220;Arteries&#8221; of the Earth, coupling the biogeochemical cycling of continents and oceans. Frequent human activities usually increase nitrogen load, and nitrifying microorganisms are crucial for the management of nitrogen load in rivers. The ecological roles of truncated nitrifiers, including canonical ammonia-oxidizing bacteria, ammonia-oxidizing archaea and nitrite-oxidizing bacteria in rivers have been fully understood, however, investigations of the newly discovered comammox Nitrospira are very scarce. To fill this gap, we used the metagenomic shotgun sequencing to provide the first biogeographic patterns of comammox Nitrospira in the Yangtze River over a 6030 km continuum.First, ten novel comammox genomes (71~96% completeness) were reconstructed with the metagenome assemblies from fluvial water in the upper reach and surface sediments from the middle reach to the estuary. Gene arrangements in ammonia oxidation-related gene clusters of these novel genomes were more complex and diverse than those of the previously discovered ones. For instance, multi-copy amoA or amoB genes, peptidases, cupredoxin and fkpA-cytochrome c-nirK gene sets were first found within the ammonia oxidation-related gene clusters of comammox Nitrospira, which might confer them advantages in adapting to the relatively oligotrophic environments and stabilizing the ammonia-oxidation process in rivers. Taxonomic analysis demonstrated that all riverine comammox genomes (constituting four new species) belonged to clade A. Based on the phylogenies of their 37 &#8220;elite&#8221; conserved marker genes, we further separated all reported comammox clade A into five sublineages, named clade A-Ia, A-Ib, A-Ic and A-IIa, A-IIb. The reclassified sublineages were sufficiently divergent to be meaningful in expanding the taxonomic/functional diversity and improving the phylogenetic resolution.Second, based on the improved phylogenetic resolution, we explored the biogeographic patterns of planktonic and benthic comammox Nitrospira subjected to natural and anthropogenic factors along the Yangtze River. Our study revealed the wide existence of comammox Nitrospira and their significant contributions to nitrifier abundances, constituting 30% and 46% of ammonia-oxidizing prokaryotes (AOPs) and displaying 30.4- and 17.9-fold greater abundances than canonical Nitrospira representatives in water and sediments, respectively. Comammox Nitrospira were found to contribute more to nitrifier abundances (34~87% of AOPs) in typical oligotrophic environments with a higher pH and lower temperature, particularly in the plateau (clade B), mountain and foothill (clade A-Ic) of the upper reach. Environmental selection determined the niche replacement of planktonic comammox Nitrospira by canonical ammonia-oxidizing bacteria and Nitrospira sublineages I/II from upstream to downstream, leading to a higher spatial turnover rate than observed for the benthic counterpart, while the dissimilarity of benthic comammox Nitrospira was moderately driven by geographic distance. A considerable decrease (83%) in benthic comammox Nitrospira abundance occurred immediately downstream of the Three Gorges Dam, which was consistent with a substantial decrease in the overall bacterial taxa in sediments.Together, this study highlights the previously unrecognized dominance of comammox Nitrospira in major river systems and underlines the importance of revisiting the distributions of and controls on nitrification processes within global freshwater environments.

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Abundance and composition of ammonia-oxidizing bacteria and archaea in different types of soil in the Yangtze River estuary

Journal of Zhejiang University SCIENCE B ◽

10.1631/jzus.b1200013 ◽

2012 ◽

Vol 13 (10) ◽

pp. 769-782 ◽

Cited By ~ 18

Author(s):

Xiao-ran Li ◽

Yi-ping Xiao ◽

Wen-wei Ren ◽

Zeng-fu Liu ◽

Jin-huan Shi ◽

...

Keyword(s):

Yangtze River ◽

River Estuary ◽

Yangtze River Estuary ◽

Ammonia Oxidizing Bacteria ◽

The Yangtze River ◽

The Yangtze River Estuary ◽

Different Types

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Integrated biogeography and assembly process of planktonic and sedimentary bacterial communities in the Yangtze River

10.5194/egusphere-egu2020-4567 ◽

2020 ◽

Author(s):

Tang Liu ◽

Jiawen Wang ◽

Shufeng Liu ◽

Qian Chen ◽

Chunmiao Zheng ◽

...

Keyword(s):

Bacterial Communities ◽

Yangtze River ◽

Selection Process ◽

Anthropogenic Impacts ◽

Spatiotemporal Pattern ◽

Assembly Process ◽

The Yangtze River ◽

Species Sorting ◽

Biogeographic Patterns ◽

Water And Sediment

Bacterial communities are essential to the biogeochemical cycle in riverine ecosystems. However, the integrated biogeography and assembly process of planktonic and sedimentary bacterial communities in large rivers is still poorly understood. Here, the study provided the spatiotemporal pattern of bacterial communities in the Yangtze River of 4300 km continuum, which is the largest river in Asia. We found that the taxa in sediments are the main contributors to the bacterial diversity of the river ecosystem since sediments sub-group took 98.8% of the total 38, 904 Operational Taxonomic Units (OTUs) observed in 280 samples. Seasonal differences in bacterial communities were statistically significant in water, whereas bacterial communities in both water and sediment were geographically clustered according to five types of landforms: mountain, foothill, basin, foothill-mountain, and plain. Interestingly, the presence of two huge dams resulted in a drastic fall of bacterial taxa in sediment immediately downstream due to severe riverbed scouring. The integrity of the biogeography was satisfactorily interpreted by the combination of neutral and species sorting perspectives in meta-community theory for bacterial communities in flowing water and sediment. Although deterministic process had dominant influence on assembly processes in water and sediment communities, homogeneous selection was the main contributor in water, while combination of homogeneous selection and variable selection contributed selection process in sediment. In addition, homogenizing dispersal played more important role in community assembly process in sediment than water. Our study fills a gap in understanding of biogeography and assembly process of bacterial communities in one of the world&#8217;s largest river and highlights the importance of both planktonic and sedimentary communities to the integrity of bacterial biogeographic patterns in a river subject to varying natural and anthropogenic impacts.

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Evaluation of genetic diversity and population structure of five yellow catfish Pelteobagrus fulvidraco populations by microsatellite markers

Oceanological and Hydrobiological Studies ◽

10.1515/ohs-2018-0011 ◽

2018 ◽

Vol 47 (2) ◽

pp. 99-106 ◽

Cited By ~ 1

Author(s):

Liqiang Zhong ◽

Minghua Wang ◽

Jianlin Pan ◽

Daming Li ◽

Shengkai Tang ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Yangtze River ◽

Geographic Distance ◽

Pelteobagrus Fulvidraco ◽

Freshwater Species ◽

The Yangtze River ◽

Stock Management ◽

Yellow Catfish ◽

Wild Stock

Abstract Yellow catfish, Pelteobagrus fulvidraco, is an important commercial freshwater species in China. Knowledge about the genetic diversity of the yellow catfish is important to support the management and conservation programs, which would subsequently support the sustainable production of this species. To investigate the genetic diversity and the structure of yellow catfish in the middle and lower reaches of the Yangtze River, 125 individuals from five lakes were genotyped using 13 microsatellite markers. Moderate genetic diversity was determined in all populations, with the observed heterozygosity (HO) ranging from 0.42 to 0.49 and the expected heterozygosity (HE) ranging from 0.51 to 0.61. Low to moderate genetic differentiation among the populations was revealed from pairwise FST values (p < 0.05), as well as from analysis of molecular variance (AMOVA). The UPGMA dendrogram and Bayesian clustering analysis indicated a correlation between genetic differences and geographic distance – four populations from the lower reaches clustered together, whereas the Poyang Lake (PY) population formed a separate cluster. The present study would be helpful in the wild stock management and artificial propagation programs for yellow catfish in the middle and lower reaches of the Yangtze River.

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