Inagaki, F., Suzuki, M., Takai, K., Oida, H., Sakamoto, T., Aoki, K., et al. Science 340, 1223–1226. Because of river runoff, estuaries harbor many types of terrestrial and marine subgroups of Bathyarchaeota (Zhou et al., 2018a). Commun. The influence of salinity and ammonium levels on amoA mRNA expression of ammonia-oxidizing prokaryotes. Overview of hypoxia around the world. doi: 10.1073/pnas.1605501113, Könneke, M., Bernhard, A. E., José, R., Walker, C. B., Waterbury, J. These include: Thaumarchaeota, which comprise ammonia oxidizing archaea (AOA), one of the key players of ammonia oxidation in estuaries (Francis et al., 2005; Liu L. et al., 2011; Liu Z. et al., 2011; Zou et al., 2019, 2020b); Bathyarchaeota (formerly called Miscellaneous Crenarchaeotal Group, MCG), which are hypothesized to be important players in the benthic carbon cycle that, based on genomic analysis, may be able to utilize diverse organic substrates (Meng et al., 2014; Lazar et al., 2015, 2016; He et al., 2016; Zhou et al., 2018a); Euryarchaeota, e.g., most methanogens and anaerobic methanotrophs, are responsible for methane production and oxidation in estuaries, respectively (Oremland and Polcin, 1982; Serrano-Silva et al., 2014); and Asgard archaea, such as Thorarchaeota and Lokiarchaeota, which may participate in some biogeochemical cycles, as suggested by metagenomics (Seitz et al., 2016; Liu Y. et al., 2018; MacLeod et al., 2019; Cai et al., 2020). Similarly, a recent report revealed seasonal variations of archaeal communities in estuarine and coastal regions (Liu et al., 2020), highlighting the notion that spatiotemporal distribution of archaeal community is co-influenced by environmental parameters, including salinity and temperature. The ecological functioning of estuaries depends on inflows from both the adjacent coastal marine waters as well as freshwater inflows from the river basin upstream. 12, 1473–1485. Environ. doi: 10.1038/ismej.2013.174, Merbt, S. N., Stahl, D. A., Casamayor, E. O., Martí, E., Nicol, G. W., and Prosser, J. I. Imachi, H., Nobu, M. K., Nakahara, N., Morono, Y., Ogawara, M., Takaki, Y., et al. Estuaries are also a source of inspiration, rejuvenation, and discovery. (2016). Andersson, M. G., van Rijswijk, P., and Middelburg, J. J. Please see Supplementary Tables S2, S4 for details. 7, 191–204. Environ. doi: 10.1038/ismej.2015.143, Fillol, M., Sànchez-Melsió, A., Gich, F., and Borrego, C. M. (2015). doi: 10.1038/s41561-018-0221-6. Instead, it contributes to the detrital food chain whereby it is colonized by bacteria and fungi which convert the often indigestible carbon material into more easily assimilable carbohydrates and proteins. Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia. Peng, X., Jayakumar, A., and Ward, B. Methanogenesis accounts for a large portion of global methane emission. Meng, J., Xu, J., Qin, D., He, Y., Xiao, X., and Wang, F. (2014). Res. 66, 181–196. Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean. Our estuaries are beautiful, rich in plants and animals, they attract visitors, sustain our livelihoods and uplift our spirits. Estuarize-WIO will provide a deeper understanding of SES in estuaries, as basis for strengthening co-management at ecosystem level; Estuarize-WIO Main objectives . (2019). Coupled biogeochemical cycles: eutrophication and hypoxia in temperate estuaries and coastal marine ecosystems. Ammonia oxidation is not required for growth of Group 1.1 c soil Thaumarchaeota. 69, 7224–7235. (2018a) proposed 26 subgroups for this highly diverse phylum, and suggested oxygen might as a significant factor driving the distribution and evolution of Woesearchaeota. Microbiol. doi: 10.1038/nature12352, Rodriguez-Brito, B., Rohwer, F., and Edwards, R. A. Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea. A comparison of an estuarine flora and fauna with that of a neighboring marine reef will show that there are many species, both plant and animal, which are either excluded by these changing conditions or avoid estuaries. However, most of these hypotheses are drawn based on limited genomic information. • Fish larvae detected short-time events of hydrological or water quality alterations. Mar. (2013). Hence, more detailed studies are needed to comprehensively describe their physiology. Aqu. This led to the recognition of the superphylum DPANN, as most of these microbes have small genomes and limited metabolic capacity (Rinke et al., 2013; Castelle et al., 2015). Global biogeographic analysis of methanogenic archaea identifies community-shaping environmental factors of natural environments. (2019). Diversity of Miscellaneous Crenarchaeotic Group archaea in freshwater karstic lakes and their segregation between planktonic and sediment habitats. Ser. Recently, Liu et al. Physiol. 20, 734–754. Generally, based on the Cluster of Orthologous Groups (COG) categories, estuarine AOA have a higher proportion of genomic content related to transport and metabolism of amino acids, nucleotides, and lipids than marine AOA (Ngugi et al., 2015). doi: 10.2134/jeq2001.302275x, Ding, J., Zhang, Y., Wang, H., Jian, H., Leng, H., and Xiao, X. FEMS Microbiol. Asgard archaea capable of anaerobic hydrocarbon cycling. Microbiol. 54, 460–468. doi: 10.1111/j.1462-2920.2010.02218.x, Mosier, A. C., Allen, E. E., Kim, M., Ferriera, S., and Francis, C. A. (2013). Liu et al. doi: 10.1016/S0025-326X(02)00474-5, Huber, H., Hohn, M. J., Rachel, R., Fuchs, T., Wimmer, V. C., and Stetter, K. O. For example, Woesearchaeota might support the growth of some H2/CO2-using and acetate-using methanogens to compete with hydrogenotrophic and acetotrophic methanogens, in exchange receiving amino-acids and other compounds (Liu et al., 2018a). (2016) suggested that members of Bathyarchaeota (Bathy-13, -16, -21, and -22) are acetogens and can utilize diverse organic substrates for fermentation. doi: 10.1128/aem.44.6.1270-1276.1982, Pan, J., Chen, Y., Wang, Y., Zhou, Z., and Li, M. (2019). 72, 7767–7777. Ecol. 373, 591–599. Copyright © 2020 Zou, Liu and Li. Biotechnol. Among them, Thaumarchaeota and Bathyarchaeota are more abundant in water columns and sediments, respectively, while Euryarchaeota inhabit both aquatic and sedimentary environments. Archaea are currently understood to be ubiquitously distributed in diverse environments, and are recognized as important players in the global biogeochemical cycles. (2016). Based on the amoA genotypes as suggested by Alves et al. The complex relationship between these two inputs determines, to a large extent, the nature of the estuarine ecosystem and associated services which are provided by that ecosystem. Microbiol. Environ. Microbial activities in estuaries are stimulated by numerous nutrients carried by a river discharge (Milliman et al., 1985), that may favor the growth of estuarine microbes, including archaea. Sci. Estuaries are areas meets the seawater has high salinity and low salinity of the river water. 10, 665–677. An estimate of global primary production in the ocean from satellite radiometer data. 15, 2545–2556. This indicates not all AOA are obligate autotrophic ammonia oxidizers under certain conditions. The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. Child wellbeing was measured by the Unicef index of child wellbeing. 14, 805–822. Further, genes related to signal transduction and regulation mechanisms are significantly enriched in the epipelagic clade compared with the mesopelagic clade (Rodriguez-Brito et al., 2006), which may be crucial for their adaptation to the changing upper oceanic environment. (2018a). The abundance and transcription of bacterial amoA genes are reduced with decreasing dissolved oxygen (DO), but DO changes do not significantly influence the diversity of archaeal amoA genes (Abell et al., 2011). Microbiol. 18, 1200–1211. Asgard archaea are considered as the bridge between eukaryotes and prokaryotes because they are phylogenetically close to eukaryotic cells and encode many genes related to eukaryotic signature proteins (Zaremba-Niedzwiedzka et al., 2017). doi: 10.1371/journal.pone.0231238, Daebeler, A., Herbold, C. W., Vierheilig, J., Sedlacek, C. J., Pjevac, P., Albertsen, M., et al. Microb. Proc. Coast. Marine waters cover more than 70% of the surface of the Earth and account for more than 97% of Earth's water supply and 90% of habitable space on Earth. Nature 541, 353–358. Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen. doi: 10.1111/j.1574-6968.2011.02457.x, Milliman, J. D., Huang-Ting, S., Zuo-Sheng, Y., and Mead, R. H. (1985). 28, 1405–1415. Managing Estuaries in South Africa: A step by step guide. Acad. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. (2014). U.S.A. 107, 8806–8811. In addition, some Bathyarchaeota may reduce S0 to sulfide using the hydrogenase/sulfur reductase (hydA), while members of Bathy-15 and -17 encode genes related to sulfate reduction and some Bathy-6 genomes harbor thiosulfate reduction genes (Pan et al., 2020). (2014). DeLong, E. F., and Pace, N. R. (2001). Estuaries usually harbor a highly diverse active microbial community, largely because of the mixing of terrestrial and oceanic species via river runoff. Advances in culture-independent technologies facilitate the research into most archaeal groups, which expands our understanding of their diversity, distribution, metabolic potentials, and ecological niches. An estuary is a unique and complex ecosystem with the presence of various habitat types. For example, archaeal amoA genes are more abundant in low-salinity sediments of the San Francisco Bay than in high salinity regions (Mosier and Francis, 2008), but show positive correlation with salinity in the Elkhorn Slough Estuary (Caffrey et al., 2007). Tourism Fisheries and other commercial activities thrive on the wealth of natural resources estuaries supply. Xiang, X., Wang, R., Wang, H., Gong, L., Man, B., and Xu, Y. Some of its members have been hypothesized to have mutualistic or parasitic lifestyles (Baker et al., 2010; Rinke et al., 2013; Castelle et al., 2015; Eme and Doolittle, 2015; Dombrowski et al., 2019). These macrophytes all contribute to the formation of a three dimensional environment and thereby provide major habitat types for sheltering small fish and invertebrates. 11, 1118–1129. Interaction studies of vegetation within flow environments are essential for the determination of bank protection, morphological characteristics and ecological conditions for wetlands. Generally, each subgroup falls into a family or order level based on the 16S rRNA genes (Yarza et al., 2014), while the classification of subgroups varies in different studies. Microbiol. 78, 7501–7510. 11:2060. doi: 10.3389/fmicb.2020.02060. Nature 577, 519–525. Hence, they are not directly comparable to each other unless all these issues are carefully considered. This report examines these ecological aspects of the estuary but also encompasses land areas having a direct interrelationship with the biological transition zones described above. Many environmental factors drive the archaeal distribution in estuaries, such as geographic location, salinity, and oxygen levels, while the response to these factors varies among the different archaeal groups. 11, 2407. doi: 10.1038/ismej.2017.122, Alla, A. Archaeal community diversity and abundance changes along a natural salinity gradient in estuarine sediments. doi: 10.1128/aem.00946-06, Bernhard, A. E., and Bollmann, A. (2020). Microbiol. A. doi: 10.1093/femsre/fuy023, Zhou, Z., Zhang, G. X., Xu, Y. FEMS Microbiol. Lett. (2013). doi: 10.1111/j.1574-6941.2010.00988.x, PubMed Abstract | CrossRef Full Text | Google Scholar, Abril, G., and Borges, A. V. (2005). 30, 275–281. doi: 10.1093/plankt/17.6.1245, Lu, Z., Gan, J., Dai, M., Liu, H., and Zhao, X. Recently, members of Bathy-6, -8, and -20 were found to encode potential anaerobic cobalamin biosynthesis pathways (Pan et al., 2020). Bathy-8 usually dominates in marine sediments and at greater depth (Lazar et al., 2016; Yu et al., 2017), while also dominating in the near-shore surface sediment samples in the northern East China Sea (Chen Y. et al., 2020). Diversity and abundance of Korarchaeota in terrestrial hot springs of Iceland and Kamchatka. ISME J. Global Biogeochem. (2011). Salinity and other environmental parameters are important for shaping the bathyarchaeotal community in costal and estuarine regions (Liu et al., 2014; Lazar et al., 2015; Yoshimura et al., 2018; Zhou et al., 2018b; Pan et al., 2019; Chen Y. et al., 2020; Zou et al., 2020b). (2019) compared genomic capacities of 10 bathyarchaeotal subgroups, and suggested that most Bathyarchaeota generally lead a lifestyle relying on both heterotrophic degradation and autotrophic carbon fixation. However, other than spatial and temporal variables, technical biases, such as sampling methods, library construction approaches, and different usage of primers and marker genes, might also impact the microbial community composition. Them is subject to rapid and sometimes extreme changes differing histories of hypoxia west off the River! L. ( 2015 ) bores cause great damage to the northern South China Sea Sweeney, C., and,!, Wang, F. ( 2017 ) identified several indicator subgroups in estuaries we must not. 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