1
|
Biogeochemical Responses and Seasonal Dynamics of the Benthic Boundary Layer Microbial Communities during the El Niño 2015 in an Eastern Boundary Upwelling System. WATER 2021. [DOI: 10.3390/w13020180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Eastern South Pacific coastal zone is characterized by seasonal and interannual variability, driven by upwelling and El Niño Southern Oscillation (ENSO), respectively. These oceanographical conditions influence microbial communities and their contribution to nutrient and greenhouse gases recycling, especially in bottom waters due to oxygenation. This article addresses the seasonal hydrographic and biogeochemical conditions in the water and sediments during El Niño 2015. Bottom water active microbial communities, including nitrifiers, were studied using amplicon sequencing of 16S rRNA (cDNA) and RT-qPCR, respectively. The results of the hydrographic analysis showed changes in the water column associated with the predominance of sub-Antarctic Waters characterized by warmed and low nutrients in the surface and more oxygenated conditions at the bottom in comparison with El Niño 2014. The organic matter quantity and quality decreased during fall and winter. The bottom water active microbial assemblages were dominated by archaea (Ca. Poseidoniales) and putative ammonia oxidizing archaea. Active bacteria affiliated to SAR11, Marinimicrobia and Nitrospina, and oxygen deficient realms (Desulfobacterales, SUP05 clade and anammox) suffered variations, possibly associated with oxygen and redox conditions in the benthic boundary layer. Nitrifying functional groups contributed significantly more during late fall and winter which was consistent with higher bottom water oxygenation. Relationships between apparent oxygen utilization nitrate and nitrous oxide in the water support the contribution of nitrification to this greenhouse gas distribution in the water. In general, our study suggests that seasonal oceanographic variability during an El Niño year influences the microbial community and thus remineralization potential, which supports the need to carry out longer time series to identify the relevance of seasonality under ENSO in Eastern Boundary Upwelling Systems (EBUS) areas.
Collapse
|
2
|
Mao TQ, Li YQ, Dong HP, Yang WN, Hou LJ. Spatio-Temporal Variations in the Abundance and Community Structure of Nitrospira in a Tropical Bay. Curr Microbiol 2020; 77:3492-3503. [PMID: 32929577 DOI: 10.1007/s00284-020-02193-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/01/2020] [Indexed: 01/20/2023]
Abstract
Nitrospira is the most diverse genus of nitrite-oxidizing bacteria, and its members are widely spread in various natural and engineered ecosystems. In this study, the phylogenetic diversity of Nitrospira and monthly changes of its abundance from Zhanjiang Bay were investigated. Phylogenetic analysis showed that among 58 OTUs with high abundance, 74% were not affiliated with any previously described Nitrospira species, revealing a previously unrecognized diversity of coastal Nitrospira. The abundances of both Nitrospira and Nitrospina exhibited a significantly monthly change. During most of the months, abundance of Nitrospina was greater than that of Nitrospira. In particle-attached communities, either abundance of Nitrospina or Nitrospira was highly correlated with that of ammonia-oxidizing archaea (AOA), whereas abundance of ammonia-oxidizing bacteria was only highly correlated with that of Nitrospina. In free-living communities, either abundance of Nitrospina or Nitrospira was correlated only with that of AOA. These results suggest that both Nitrospira and Nitrospina can be involved in nitrite oxidation by coupling with AOA, but Nitrospina may play a greater role than Nitrospira in this tropical bay.
Collapse
Affiliation(s)
- Tie-Qiang Mao
- School of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yan-Qun Li
- School of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Hong-Po Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China. .,Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200061, China.
| | - Wen-Na Yang
- School of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| |
Collapse
|
3
|
Cornejo-D'Ottone M, Molina V, Pavez J, Silva N. Greenhouse gas cycling by the plastisphere: The sleeper issue of plastic pollution. CHEMOSPHERE 2020; 246:125709. [PMID: 31901660 DOI: 10.1016/j.chemosphere.2019.125709] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/12/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
Plastic is an allochthonous material to marine ecosystems but is rapidly colonized by marine microbial communities, with an as yet unclear contribution to biogeochemical cycles. In this study, we investigated the influence of an active microbial community grown on microplastic particles (the plastisphere) on CO2 and N2O recycling and its potential role in greenhouse gas inventories and air-sea exchange. Microplastics were collected during two cruises (Cimar 21 and FIP Montes Submarinos) from the surface layer (5 m depth) from several contrasting trophic regions of the South Pacific Ocean, i.e., from a transition zone off the eutrophic coastal upwelling of Chile, to a mesotrophic transition area of oceanic seamounts and, finally, to an oligotrophic zone in the South Pacific Subtropical Gyre. . Experiments were carried out onboard to evaluate CO2 and N2O production/consumption by the plastisphere. The active microbial community and its specific quantification were determined for Cimar 21 using iTag 16 S rRNA. The experiments showed that the plastisphere generally contributed to CO2 and N2O production/consumption, with rates ranging from -20.5 (consumption) to +4.5 (production) μmol/m2/d. The seamounts and the transition zone presented the highest production/consumption rates. The experiments performed in the two seamount stations showed that production and consumption of CO2 were related to the environmental nutrient concentration. Both stations presented N2O consumption that was associated with the high nitrogen deficit of the subantarctic water mass. The transition zone presented CO2 and N2O production in a plastisphere dominated by heterotrophic communities. The plastisphere in oligotrophic waters was diverse and active. The experiments, however, presented low or no production of greenhouse gases. Our results show a contribution of CO2 and N2O to the global gas surface inventories and air-sea exchange is lower than 1% of the global sources. These results highlight different critical impacts of plastic pollution on the environment that have, until now, not been considered.
Collapse
Affiliation(s)
- Marcela Cornejo-D'Ottone
- Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso and Instituto Milenio de Oceanografía, Chile.
| | - Verónica Molina
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Chile
| | - Javiera Pavez
- Programa de Magister en Oceanografía, Pontificia Universidad Católica de Valparaíso, Chile
| | - Nelson Silva
- Escuela de Ciencias del Mar, Pontificia Universidad Católica de Valparaíso, Chile
| |
Collapse
|
4
|
Xu S, Wang B, Li Y, Jiang D, Zhou Y, Ding A, Zong Y, Ling X, Zhang S, Lu H. Ubiquity, diversity, and activity of comammox Nitrospira in agricultural soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135684. [PMID: 31862588 DOI: 10.1016/j.scitotenv.2019.135684] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/20/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
The recent discovery of complete ammonia oxidation (comammox) process in a single organism challenged the division of labor between two functional groups in the classical two-step nitrification model. However, the distribution and activity of comammox bacteria in various environments remain largely unknown. This study presented a large-scale investigation of the geographical distribution, phylogenetic diversity, and activity of comammox Nitrospira in typical agricultural soils. Among the 23 samples harvested across China, comammox Nitrospira clade A was ubiquitously detected at 4.14 × 104-1.65 × 107amoA gene copies/g dry soil, with 90% belonging to the subclade A2. The abundance of comammox Nitrospira clade B was two orders of magnitude lower than clade A. In all samples, comammox Nitrospira were 1-2 orders of magnitude less abundant than canonical nitrifiers, and soils with slightly high pH and C/N tended to enrich more comammox Nitrospira. Unlike canonical nitrifiers, comammox Nitrospira had sustained amoA gene transcription regardless of external ammonia supply, indicating their competitive advantage over other nitrifiers under low-ammonia conditions. When fed with 1 mM ammonium for 15 days, comammox Nitrospira in tested soils were enriched 2.36 times higher than those enriched by the same amount of nitrite, indicating their preference to utilizing ammonia as the substrate. DNA-SIP further confirmed the in situ nitrification activity of comammox Nitrospira. This study provided new insights into the broad distribution and diversity of comammox Nitrospira in agricultural soils, which could potentially play an important role in the microbial nitrogen cycle in soils.
Collapse
Affiliation(s)
- Shaoyi Xu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Baozhan Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yong Li
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Daqian Jiang
- Environmental Engineering Department, Montana Tech, Butte, United States
| | - Yuting Zhou
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Aqiang Ding
- College of Resource and Environmental Science, Chongqing University, Chongqing, China
| | - Yuxiao Zong
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoting Ling
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Senyin Zhang
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Huijie Lu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
| |
Collapse
|
5
|
Yepsen DV, Levipan HA, Molina V. Nitrospina bacteria in a rocky intertidal habitat (Quintay Bay, central Chile). Microbiologyopen 2018; 8:e00646. [PMID: 29799171 PMCID: PMC6436435 DOI: 10.1002/mbo3.646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 02/27/2018] [Accepted: 03/30/2018] [Indexed: 11/06/2022] Open
Abstract
Nitrospina bacteria are among the most important nitrite oxidizers in coastal and open-ocean environments, but the relevance of the genus contrasts with the scarceness of information on their ecophysiology and habitat range. Thus far, Nitrospina bacteria have been the only nitrite oxidizers detected at high abundance in Chilean coastal waters. These levels are often higher than at other latitudes. In this study, the abundance of 16S-rRNA gene transcripts of Nitrospina (hereafter just transcripts) was measured by reverse transcription quantitative PCR in a rocky intertidal gradient and compared with the nearshore counterpart off central Chile (~33°S). Rocky pond transcripts were also compared with the taxonomic composition of the macrobiota and bacterioplankton (by 16S-rRNA gene-based T-RFLP) in the intertidal gradient. Transcripts increased from warmer, saltier, and low-nitrite ponds in the upper intertidal zone (19.5 ± 1.6°C, 39.0 ± 1.0 psu, 0.98 ± 0.17 μmol/L) toward cooler, less salty, and high-nitrite ponds (17.8 ± 2.6°C, 37.7 ± 0.82 psu, 1.23 ± 0.21 μmol/L) from middle and low zones. These varied from ~1,000 up to 62,800 transcripts. This increasing trend in the number of transcripts toward the lower zone was positively associated with the Shannon's diversity index for the macrobiota (r = .81, p < .01). Moreover, an important increase in the average number of transcripts was observed in ponds with a greater number of fish in the upper (7,846 transcripts during 2013) and lower zones (62,800 transcripts during 2015). Altogether, intertidal and nearshore transcripts were significantly correlated with nitrite concentrations (r = .804, p ˂ .01); rocky pond transcripts outnumbered nearshore ones by almost two orders of magnitude. In summary, rocky ponds favored both the presence and activity of Nitrospina bacteria that are tolerant to environmental stress. This in turn was positively influenced by the presence of ammonia- or urea-producing macrobiota.
Collapse
Affiliation(s)
- Daniela V Yepsen
- Programa de Doctorado en Ciencias con mención en Manejo de Recursos Acuáticos Renovables, Universidad de Concepción, Concepción, Chile
| | - Héctor A Levipan
- Centro de Investigación Marina Quintay (CIMARQ), Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Valparaíso, Chile
| | - Verónica Molina
- Programa de Biodiversidad, Departamento de Biología, Observatorio de Ecología Microbiana, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile
| |
Collapse
|
6
|
Wan XS, Sheng HX, Dai M, Zhang Y, Shi D, Trull TW, Zhu Y, Lomas MW, Kao SJ. Ambient nitrate switches the ammonium consumption pathway in the euphotic ocean. Nat Commun 2018; 9:915. [PMID: 29500422 PMCID: PMC5834513 DOI: 10.1038/s41467-018-03363-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/08/2018] [Indexed: 12/03/2022] Open
Abstract
Phytoplankton assimilation and microbial oxidation of ammonium are two critical conversion pathways in the marine nitrogen cycle. The underlying regulatory mechanisms of these two competing processes remain unclear. Here we show that ambient nitrate acts as a key variable to bifurcate ammonium flow through assimilation or oxidation, and the depth of the nitracline represents a robust spatial boundary between ammonium assimilators and oxidizers in the stratified ocean. Profiles of ammonium utilization show that phytoplankton assemblages in nitrate-depleted regimes have higher ammonium affinity than nitrifiers. In nitrate replete conditions, by contrast, phytoplankton reduce their ammonium reliance and thus enhance the success of nitrifiers. This finding helps to explain existing discrepancies in the understanding of light inhibition of surface nitrification in the global ocean, and provides further insights into the spatial linkages between oceanic nitrification and new production. The underlying regulatory mechanisms of phytoplankton assimilation and microbial oxidation of ammonium in the surface ocean are unclear. Here, using isotope labeling experiments, the authors show that ambient nitrate is a key variable bifurcating ammonium flow through assimilation or oxidation.
Collapse
Affiliation(s)
- Xianhui Sean Wan
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China
| | - Hua-Xia Sheng
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China
| | - Minhan Dai
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China
| | - Dalin Shi
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China
| | - Thomas W Trull
- Antarctic Climate and Ecosystems Cooperative Research Centre, University of Tasmania, and CSIRO Oceans and Atmosphere, Hobart, 7001, Australia
| | - Yifan Zhu
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China
| | - Michael W Lomas
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, 361101, Xiamen, China.
| |
Collapse
|