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Joe EN, Chae HG, Rehman JU, Oh MS, Yoon HY, Shin HJ, Kim PJ, Lee JG, Gwon HS, Jeon JR. Methane emissions and the microbial community in flooded paddies affected by the application of Fe-stabilized natural organic matter. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169871. [PMID: 38185178 DOI: 10.1016/j.scitotenv.2024.169871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/12/2023] [Accepted: 01/01/2024] [Indexed: 01/09/2024]
Abstract
Redox chemistry involving the quinone/phenol cycling of natural organic matter (NOM) is known to modulate microbial respiration. Complexation with metals or minerals can also affect NOM solubilization and stability. Inspired by these natural phenomena, a new soil amendment approach was suggested to effectively decrease methane emissions in flooded rice paddies. Structurally stable forms of NOM such as lignin and humic acids (HAs) were shown to decrease methane gas emissions in a vial experiment using different soil types and rice straw as a methanogenic substrate, and this inhibitory behavior was likely enhanced by ferric ion-NOM complexation. A mechanistic study using HAs revealed that complexation facilitated the slow release of the humic components. Interestingly, borohydride-based reduction, which transformed quinone moieties into phenols, caused the HAs to lose their inhibitory capacity, suggesting that the electron-accepting ability of HAs is vital for their inhibitory effect. In rice field tests, the humic-metal complexes were shown to successfully mitigate methane generation, while carbon dioxide emissions were relatively unchanged. Microbial community analysis of the rice fields by season revealed a decrease in specific cellulose-metabolizing and methanogenic genera associated with methane emissions. In contrast, the relative abundance of Thaumarchaeota and Actinomycetota, which are associated with NOM and recalcitrant organics, was higher in the presence of Fe-stabilized HAs. These microbial dynamics suggest that the slow release of humic components is effective in modulating the anoxic soil microbiome, possibly due to their electron-accepting ability. Given the simplicity, cost-effectiveness, and soil-friendly nature of complexation processes, Fe-stabilized NOM represents a promising approach for the mitigation of methane emissions from flooded rice paddies.
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Affiliation(s)
- Eun-Nam Joe
- Department of Agricultural Chemistry and Food Science & Technology, Division of Applied Life Science (BK21), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Ho Gyeong Chae
- Department of Agricultural Chemistry and Food Science & Technology, Division of Applied Life Science (BK21), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jalil Ur Rehman
- Department of Agricultural Chemistry and Food Science & Technology, Division of Applied Life Science (BK21), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Min Seung Oh
- Department of Agricultural Chemistry and Food Science & Technology, Division of Applied Life Science (BK21), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Ho Young Yoon
- Department of Agricultural Chemistry and Food Science & Technology, Division of Applied Life Science (BK21), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Ho-Jun Shin
- Department of Agricultural Chemistry and Food Science & Technology, Division of Applied Life Science (BK21), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Pil Joo Kim
- Department of Agricultural Chemistry and Food Science & Technology, Division of Applied Life Science (BK21), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jeong Gu Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyo Suk Gwon
- Department of Climate Change and Agroecology, National Institute of Agricultural Science, Wanju 55365, Republic of Korea.
| | - Jong-Rok Jeon
- Department of Agricultural Chemistry and Food Science & Technology, Division of Applied Life Science (BK21), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea.
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Tian Z, Zhao M, Sui X, Li X, Qin L, Chen ZJ, Zhao S, Zhao H. Associations between vaginal microbiota and endometrial polypoid lesions in women of reproductive age: a cross-sectional study. Reprod Biomed Online 2024; 48:103602. [PMID: 38101145 DOI: 10.1016/j.rbmo.2023.103602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/04/2023] [Accepted: 10/03/2023] [Indexed: 12/17/2023]
Abstract
RESEARCH QUESTION What are the different characteristics of vaginal microbial composition between patients with endometrial polypoid lesions and controls? DESIGN This cohort study compared the pre-operative microbial compositions of vaginal samples in a cohort of 703 women with endometrial polypoid lesions [293 and 410 women diagnosed and not diagnosed with polyps pathologically (polyps group and not-polyps group, respectively] and 703 women in the control group. Bacterial abundance, diversity, differential taxa and microbial network structure were assessed using 16S rRNA gene sequencing. Predictive algorithms were used to determine the functional pathways of vaginal microbiota within the cohort. RESULTS The control group exhibited higher relative abundance of Lactobacillus crispatus in comparison with the polypoid lesions group (P = 0.0427). Beta diversity of vaginal microbiota differed significantly between the groups (P < 0.05). Comparing the polyps group with the not-polyps group, Leptotrichia spp. and Cutibacterium spp. were more abundant in the polyps group, and Fannyhessea spp., Acinetobacter spp. and Achromobacter spp. were more abundant in the not-polyps group. The control group exhibited higher abundance of Bifidobacterium spp., Achromobacter spp. and Escherichia/Shigella spp. (false discovery rate < 0.05). Furthermore, the polyps group and not-polyps group displayed more complex co-occurrence networks compared with the control group. CONCLUSIONS The results of this study provide compelling evidence supporting associations between vaginal microbiota and endometrial polypoid lesions, highlighting the potential relationship between a well-balanced vaginal microbial ecosystem and a healthy intrauterine environment.
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Affiliation(s)
- Zhaomei Tian
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Maoning Zhao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Xinlei Sui
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Xiao Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Lang Qin
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China
| | - Zi-Jiang Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China; Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, China; Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China; Centre for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shigang Zhao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China; Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, China; Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Han Zhao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China; Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China; National Research Centre for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China; Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, Jinan, Shandong, China; Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China.
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Sun C, Zhang S, Yang J, Zhou H, Cheng H, Chen Z, Yu L, Wang Y, Chen X. Discrepant assembly processes of prokaryotic communities between the abyssal and hadal sediments in Yap Trench. ENVIRONMENTAL RESEARCH 2024; 241:117602. [PMID: 37951379 DOI: 10.1016/j.envres.2023.117602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/17/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
Abyssal and hadal sediments represent two of the most type ecosystems on Earth and have the potential interactions with geochemistry. However, little is known about the prokaryotic community assembly and the response of prokaryotic communities to metal(loid)s in trench sediments due to the lack of adequate and appropriate samples. In this study, a systematic investigation combined the assembly mechanisms and co-occurrence patterns of prokaryotic communities between the hadal and abyssal sediments across the Yap Trench. The results revealed that the hadal prokaryotes had less species diversity, but more abundant function than the abyssal prokaryotes. The prokaryotic communities in the abyssal sediments had more core taxa than the hadal sediments. Twenty-one biomarkers mostly affiliated with Nitrosopumilaceae were detected using Random-Forests machine learning algorithm. Furthermore, stochasticity was dominant in the prokaryotic community assembly processes of the Yap Trench sediments. Meanwhile, homogeneous selection (32.6%-52.9%) belonging to deterministic processes governed the prokaryotic community assembly in hadal sediments with increasing of sediment depth. In addition to total nitrogen and total organic carbon, more metal(loid)s were significantly correlated with the prokaryotic community in the hadal sediments than that in the abyssal sediments. The hadal prokaryotic communities was most positively related to bismuth (r = 0.31, p < 0.01), followed by calcium, chromium, cerium, potassium, plumbum, scandium, titanium, and vanadium. Finally, co-occurrence networks revealed two potential dominant prokaryotic modules in Yap Trench sediments covaried across oceanographic zonation. By contrast, the hadal network had relatively more complexity, more bacterial taxa, and more associations among prokaryotic taxa, relative to the abyssal network. This study reveals potentially metal variables and community assembly mechanisms of the prokaryotic community in abyssal and hadal sediments and provides a better understanding on the prokaryotic diversity and ecology in trench sediment ecosystems.
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Affiliation(s)
- Chongran Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Shuangfei Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Jichao Yang
- College of Marine Science and Engineering, Shandong University of Science and Technology, Qingdao, 266590, Shandong, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, Hunan, China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, Hunan, China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, Hunan, China
| | - Libo Yu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, Hunan, China.
| | - Xinhua Chen
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Zhang Y, Liu J, Song D, Yao P, Zhu S, Zhou Y, Jin J, Zhang XH. Stochasticity-driven weekly fluctuations distinguished the temporal pattern of particle-associated microorganisms from its free-living counterparts in temperate coastal seawater. WATER RESEARCH 2024; 248:120849. [PMID: 37979570 DOI: 10.1016/j.watres.2023.120849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Microbial community dynamics directly determine their ecosystem functioning. Despite the well-known annual recurrence pattern, little is known how different lifestyles affect the temporal variation and how community assembly mechanisms change over different temporal scales. Here, through a high-resolution observation of size fractionated samples over 60 consecutive weeks, we investigate the distinction in weekly distribution pattern and assembly mechanism between free-living (FL) and particle-associated (PA) communities in highly dynamic coastal environments. A clear pattern of annual recurrence was observed, which was more pronounced in FL compared to PA, resulting in higher temporal specificity in the former samples. Both the two size fractions displayed significant temporal distance-decay patterns, yet the PA community showed a higher magnitude of community variation between adjacent weeks, likely caused by sudden, drastic and long-lived blooms of heterotrophic bacteria. Generally, determinism (environmental selection) had a greater effect on the community assembly than stochasticity (random birth, death, and dispersal events), with significant contributions from temperature and inorganic nutrients. However, a clear shift in the temporal assembly pattern was observed, transitioning from a prevalence of stochastic processes driving short-term (within a month) fluctuations to a dominance of deterministic processes over longer time intervals. Between adjacent weeks, stochasticity was more important in the community assembly of PA than FL. This study revealed that stochastic processes can lead to rapid, dramatic and irregular PA community fluctuations, indicating weak resistance and resilience to disturbances, which considering the role of PA microbes in carbon processing would significantly affect the coastal carbon cycle. Our results provided a new insight into the microbial community assembly mechanisms in the temporal dimension.
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Affiliation(s)
- Yulin Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jiwen Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Derui Song
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266237, China; Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Shaodong Zhu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Yi Zhou
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Jian Jin
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266237, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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Lu Y, Cheung S, Koh XP, Xia X, Jing H, Lee P, Kao SJ, Gan J, Dai M, Liu H. Active degradation-nitrification microbial assemblages in the hypoxic zone in a subtropical estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166694. [PMID: 37660824 DOI: 10.1016/j.scitotenv.2023.166694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 08/06/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
In 2017 summer, we observed widespread bottom hypoxia at the lower estuary of the Pearl River estuary (PRE). Our previous study noticed that AOA and bacteria were highly abundant and clustered within the hypoxia zone. Moreover, nitrification and respiration rates were also evidently higher in these hypoxic waters. These observations prompt us to investigate whether these two oxygen-consuming microorganisms have symbiotic relationships and whether specific groups consistently coexist and form ecological-meaningful associations. In this study, we use network analysis to investigate the presence and active communities (DNA-RNA) based on bacterial and AOA communities sequencing (inferred from the 16S rRNA and amoA gene, respectively) to gain more insight into ecological-meaningful associations. We observed a highly diverse and active bacterial community in the hypoxia zone. The RNA networks were more modulized than the corresponding DNA networks, indicating that the active communities were better parsed into functional microbial assemblages. The network topology revealed that Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia, Cyanobacteria (Synechococcales), and AOA sublineages were module hubs and connectors, indicating that they were the keystone taxa of the microbial communities. The hub-subnetwork further showed robust co-occurrence between Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia with AOA sublineages, and Nitrospinae (presumably NOB) reflecting the formation of Degradation-Nitrification (sequential oxidation of Organic matter degradation to ammonia, then nitrate) microbial assemblage in the hypoxia zone. The subnetworks revealed AOA ecotype-specific modularization and niche partitioning of different AOA sublineages. Interestingly, the recurring co-occurrence of nitrifiers assemblage in the RNA subnetworks (SCM1-like-II (AOA) and Nitrospinae OTUs (NOB) suggests an active interaction via nitrite exchange. The Degradation-Nitrification microbial assemblage may contribute substantially to the oxygen consumption in the hypoxia formation in PRE. Our results provide new insight into the functional microbial assemblages, which is worth further investigation on their ecological implication in estuarine waters.
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Affiliation(s)
- Yanhong Lu
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, Guangdong; Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong; Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong; Shenzhen Marine Development and Promotion Center, Shenzhen, Guangdong.
| | - Shunyan Cheung
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
| | - Xiu Pei Koh
- Division of Environment and Sustainability, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan
| | - Puiyin Lee
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian
| | - Jianping Gan
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Minhan Dai
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong; Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong.
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Rafiq M, Hassan N, Rehman M, Hayat M, Nadeem G, Hassan F, Iqbal N, Ali H, Zada S, Kang Y, Sajjad W, Jamal M. Challenges and Approaches of Culturing the Unculturable Archaea. BIOLOGY 2023; 12:1499. [PMID: 38132325 PMCID: PMC10740628 DOI: 10.3390/biology12121499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Since Carl Woese's discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved by culturing and culture-dependent techniques. Increasing interest in demand for innovative culturing methods has led to various technological and methodological advances. The current review explains frequent hurdles hindering uncultured archaea isolation and discusses features for more archaeal cultivation. This review also discusses successful strategies and available media for archaeal culturing, which might be helpful for future culturing practices.
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Affiliation(s)
- Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
- FF Institute (Huzhou) Co., Ltd., Huzhou 313000, China
| | - Noor Hassan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-College, Pakistan Institute of Engineering and Applied Sciences, Islamabad 44000, Pakistan
| | - Maliha Rehman
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
| | - Muhammad Hayat
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Jinan 266101, China
| | - Gullasht Nadeem
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
| | - Farwa Hassan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-College, Pakistan Institute of Engineering and Applied Sciences, Islamabad 44000, Pakistan
| | - Naveed Iqbal
- Department of Biotechnology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
- The Department of Paediatrics and Child Health, Aga Khan University, Karachi 74800, Pakistan
| | - Hazrat Ali
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-College, Pakistan Institute of Engineering and Applied Sciences, Islamabad 44000, Pakistan
| | - Sahib Zada
- Guangzhou Institute of Energy Conservation, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yingqian Kang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education of Guizhou, Guiyang 550025, China
- Key Laboratory of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, China
| | - Wasim Sajjad
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University, Garden Campus, Mardan 23200, Pakistan
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Fakhraldeen SA, Al-Haddad S, Habibi N, Alagarsamy S, F. K. Habeebullah S, Ali AK, Al-Zakri WM. Diversity and spatiotemporal variations in bacterial and archaeal communities within Kuwaiti territorial waters of the Northwest Arabian Gulf. PLoS One 2023; 18:e0291167. [PMID: 37972047 PMCID: PMC10653540 DOI: 10.1371/journal.pone.0291167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/23/2023] [Indexed: 11/19/2023] Open
Abstract
Kuwaiti territorial waters of the northwest Arabian Gulf represent a unique aquatic ecosystem prone to various environmental and anthropogenic stressors that pose significant constraints on the resident biota which must withstand extreme temperatures, salinity levels, and reducing conditions, among other factors to survive. Such conditions create the ideal environment for investigations into novel functional genetic adaptations of resident organisms. Firstly, however, it is essential to identify said organisms and understand the dynamic nature of their existence. Thus, this study provides the first comprehensive analysis of bacterial and archaeal community structures in the unique waters of Kuwait located in the Northwest Arabian Gulf and analyzes their variations with respect to depth, season, and location, as well as their susceptibility to changes in abundance with respect to various physicochemical parameters. Importantly, this study is the first of its kind to utilize a shotgun metagenomics approach with sequencing performed at an average depth of 15 million paired end reads per sample, which allows for species-level community profiling and sets the framework for future functional genomic investigations. Results showed an approximately even abundance of both archaeal (42.9%) and bacterial (57.1%) communities, but significantly greater diversity among the bacterial population, which predominantly consisted of members of the Proteobacteria, Cyanobacteria, and Bacteroidetes phyla in decreasing order of abundance. Little to no significant variations as assessed by various metrics including alpha and beta diversity analyses were observed in the abundance of archaeal and bacterial populations with respect to depth down the water column. Furthermore, although variations in differential abundance of key genera were detected at each of the three sampling locations, measurements of species richness and evenness revealed negligible variation (ANOVA p<0.05) and only a moderately defined community structure (ANOSIM r2 = 0.243; p>0.001) between the various locations. Interestingly, abundance of archaeal community members showed a significant increase (log2 median ratio of RA = 2.6) while the bacterial population showed a significant decrease (log2 median ratio = -1.29) in the winter season. These findings were supported by alpha and beta diversity analyses as well (ANOSIM r2 = 0.253; p>0.01). Overall, this study provides the first in-depth analysis of both bacterial and archaeal community structures developed using a shotgun metagenomic approach in the waters of the Northwest Arabian Gulf thus providing a framework for future investigations of functional genetic adaptations developed by resident biota attempting to survive in the uniquely extreme conditions to which they are exposed.
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Affiliation(s)
- Saja A. Fakhraldeen
- Ecosystem-based Management of Marine Resources Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Salmiya, Kuwait
| | - Sakinah Al-Haddad
- Ecosystem-based Management of Marine Resources Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Salmiya, Kuwait
| | - Nazima Habibi
- Biotechnology Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Shuwaikh, Kuwait
| | - Surendraraj Alagarsamy
- Ecosystem-based Management of Marine Resources Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Salmiya, Kuwait
| | - Sabeena F. K. Habeebullah
- Ecosystem-based Management of Marine Resources Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Salmiya, Kuwait
| | - Abdulmuhsen K. Ali
- Biotechnology Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Shuwaikh, Kuwait
| | - Walid M. Al-Zakri
- Ecosystem-based Management of Marine Resources Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Salmiya, Kuwait
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Hu X, Huang Y, Gu G, Hu H, Yan H, Zhang H, Zhang R, Zhang D, Wang K. Distinct patterns of distribution, community assembly and cross-domain co-occurrence of planktonic archaea in four major estuaries of China. ENVIRONMENTAL MICROBIOME 2023; 18:75. [PMID: 37805516 PMCID: PMC10560434 DOI: 10.1186/s40793-023-00530-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/27/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND Archaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling periods are scarce. Here, we investigated the distribution, community assembly, and cross-domain microbial co-occurrence of archaea in surface waters across four major estuaries (Yellow River, Yangtze River, Qiantang River, and Pearl River) of China cross climatic zones (~ 1,800 km) during the winter and summer cruises. RESULTS The relative abundance of archaea in the prokaryotic community and archaeal community composition varied with estuaries, seasons, and stations (reflecting local environmental changes such as salinity). Archaeal communities in four estuaries were overall predominated by ammonia-oxidizing archaea (AOA) (aka. Marine Group (MG) I; primarily Nitrosopumilus), while the genus Poseidonia of Poseidoniales (aka. MGII) was occasionally predominant in Pearl River estuary. The cross-estuary dispersal of archaea was largely limited and the assembly mechanism of archaea varied with estuaries in the winter cruise, while selection governed archaeal assembly in all estuaries in the summer cruise. Although the majority of archaea taxa in microbial networks were peripherals and/or connectors, extensive and distinct cross-domain associations of archaea with bacteria were found across the estuaries, with AOA as the most crucial archaeal group. Furthermore, the expanded associations of MGII taxa with heterotrophic bacteria were observed, speculatively indicating the endogenous demand for co-processing high amount and diversity of organic matters in the estuarine ecosystem highly impacted by terrestrial/anthropogenic input, which is worthy of further study. CONCLUSIONS Our results highlight the lack of common patterns in the dynamics of estuarine archaeal communities along the geographic gradient, expanding the understanding of roles of archaea in microbial networks of this highly dynamic ecosystem.
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Affiliation(s)
- Xuya Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yujie Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Gaoke Gu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Hanjing Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Huizhen Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Huajun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, China
| | - Kai Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, School of Marine Sciences, Ningbo University, Ningbo, China.
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China.
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, China.
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9
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Thiele S, Vader A, Thomson S, Saubrekka K, Petelenz E, Müller O, Bratbak G, Øvreås L. Seasonality of the bacterial and archaeal community composition of the Northern Barents Sea. Front Microbiol 2023; 14:1213718. [PMID: 37485507 PMCID: PMC10360405 DOI: 10.3389/fmicb.2023.1213718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/15/2023] [Indexed: 07/25/2023] Open
Abstract
The Barents Sea is a transition zone between the Atlantic and the Arctic Ocean. The ecosystem in this region is highly variable, and a seasonal baseline of biological factors is needed to monitor the effects of global warming. In this study, we report the results from the investigations of the bacterial and archaeal community in late winter, spring, summer, and early winter along a transect through the northern Barents Sea into the Arctic Ocean east of Svalbard using 16S rRNA metabarcoding. Winter samples were dominated by members of the SAR11 clade and a community of nitrifiers, namely Cand. Nitrosopumilus and LS-NOB (Nitrospinia), suggest a prevalence of chemoautotrophic metabolisms. During spring and summer, members of the Gammaproteobacteria (mainly members of the SAR92 and OM60(NOR5) clades, Nitrincolaceae) and Bacteroidia (mainly Polaribacter, Formosa, and members of the NS9 marine group), which followed a succession based on their utilization of different phytoplankton-derived carbon sources, prevailed. Our results indicate that Arctic marine bacterial and archaeal communities switch from carbon cycling in spring and summer to nitrogen cycling in winter and provide a seasonal baseline to study the changes in these processes in response to the effects of climate change.
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Affiliation(s)
- Stefan Thiele
- Department of Biological Science, University of Bergen, Bergen, Norway
- Bjerknes Centre for Climate Research, Bergen, Norway
| | - Anna Vader
- University Center in Svalbard (UNIS), Longyearbyen, Norway
| | - Stuart Thomson
- University Center in Svalbard (UNIS), Longyearbyen, Norway
| | | | - Elzbieta Petelenz
- Department of Biological Science, University of Bergen, Bergen, Norway
| | - Oliver Müller
- Department of Biological Science, University of Bergen, Bergen, Norway
| | - Gunnar Bratbak
- Department of Biological Science, University of Bergen, Bergen, Norway
| | - Lise Øvreås
- Department of Biological Science, University of Bergen, Bergen, Norway
- University Center in Svalbard (UNIS), Longyearbyen, Norway
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10
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He T, Xu ZM, Wang JF, Zhang K, Wang FP, Li WL, Tian P, Li QS. Inoculation of Escherichia coli enriched the key functional bacteria that intensified cadmium accumulation by halophyte Suaeda salsa in saline soils. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131922. [PMID: 37379599 DOI: 10.1016/j.jhazmat.2023.131922] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/23/2023] [Accepted: 06/21/2023] [Indexed: 06/30/2023]
Abstract
The enhancement of cadmium (Cd) extraction by plants from contaminated soils associated with phosphate-solubilizing bacteria (PSB) has been widely reported, but the underlying mechanism remains scarcely, especially in Cd-contaminated saline soils. In this study, a green fluorescent protein-labeled PSB, the strain E. coli-10527, was observed to be abundantly colonized in the rhizosphere soils and roots of halophyte Suaeda salsa after inoculation in saline soil pot tests. Cd extraction by plants was significantly promoted. The enhanced Cd phytoextraction by E. coli-10527 was not solely dependent on bacterial efficient colonization, but more significantly, relied on the remodeling of rhizosphere microbiota, as confirmed by soil sterilization test. Taxonomic distribution and co-occurrence network analyses suggested that E. coli-10527 strengthened the interactive effects of keystone taxa in the rhizosphere soils, and enriched the key functional bacteria that involved in plant growth promotion and soil Cd mobilization. Seven enriched rhizospheric taxa (Phyllobacterium, Bacillus, Streptomyces mirabilis, Pseudomonas mirabilis, Rhodospirillale, Clostridium, and Agrobacterium) were obtained from 213 isolated strains, and were verified to produce phytohormone and promote soil Cd mobilization. E. coli-10527 and those enriched taxa could assemble as a simplified synthetic community to strengthen Cd phytoextraction through their synergistic interactions. Therefore, the specific microbiota in rhizosphere soils enriched by the inoculated PSB were also the key to intensifying Cd phytoextraction.
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Affiliation(s)
- Tao He
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Zhi-Min Xu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management Institute of Environmental and Soil Sciences, Institute of Ecoenvironmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Jun-Feng Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ke Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Fo-Peng Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Wan-Li Li
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Ping Tian
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Qu-Sheng Li
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China.
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11
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Liu J, Huang F, Liu J, Liu X, Lin R, Zhong X, Austin B, Zhang XH. Phylotype resolved spatial variation and association patterns of planktonic Thaumarchaeota in eastern Chinese marginal seas. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:257-270. [PMID: 37275536 PMCID: PMC10232715 DOI: 10.1007/s42995-023-00169-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/30/2023] [Indexed: 06/07/2023]
Abstract
The majority of marine ammonia oxidizers belong to Thaumarchaeota, a phylum of Archaea, which is distributed throughout the water column. Marine surface waters contain distinct thaumarchaeotal phylotypes compared to the deeper ocean, but spatial dynamics of the surface-associated lineages are largely unsolved. This study of 120 seawater samples from the eastern Chinese marginal seas identified contrasting distribution and association patterns among thaumarchaeotal phylotypes across different dimensions. Horizontally, Nitrosopumilus-like and Nitrosopelagicus-like phylotypes dominated the surface water (3 m) of the Yellow Sea (YS) and East China Sea (ECS), respectively, along with increased abundance of total free-living Thaumarchaeota in ECS. Similar compositional changes were observed in the surface microlayer. The spatial heterogeneity of particle-attached Thaumarchaeota was less clear in surface microlayers than in surface waters. Vertically, the Nitrosopelagicus-like phylotype increased in abundance from surface to 90 m in ECS, which led to an increase in the proportion of Thaumarchaeota relative to total prokaryotes. This occurred mainly in the free-living fraction. These results indicate a clear size-fractionated niche partitioning, which is more pronounced at lower depths than in the surface water/surface microlayer. In addition, associations of Thaumarchaeota with other microbial taxa varied between phylotypes and size fractions. Our results show that a phylotype-resolved and size-fractionated spatial heterogeneity of the thaumarchaeotal community is present in surface oceanic waters and a vertical variation of the Nitrosopelagicus-like phylotype is present in shallow shelf waters. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00169-y.
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Affiliation(s)
- Jiwen Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Fuyan Huang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China
| | - Jiao Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China
| | - Xiaoyue Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China
| | - Ruiyun Lin
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China
| | - Xiaosong Zhong
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao, 266100 China
| | - Brian Austin
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA Scotland UK
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
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12
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Jameson BD, Murdock SA, Ji Q, Stevens CJ, Grundle DS, Kim Juniper S. Network analysis of 16S rRNA sequences suggests microbial keystone taxa contribute to marine N 2O cycling. Commun Biol 2023; 6:212. [PMID: 36823449 PMCID: PMC9950131 DOI: 10.1038/s42003-023-04597-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
The mechanisms by which large-scale microbial community function emerges from complex ecological interactions between individual taxa and functional groups remain obscure. We leveraged network analyses of 16S rRNA amplicon sequences obtained over a seven-month timeseries in seasonally anoxic Saanich Inlet (Vancouver Island, Canada) to investigate relationships between microbial community structure and water column N2O cycling. Taxa separately broadly into three discrete subnetworks with contrasting environmental distributions. Oxycline subnetworks were structured around keystone aerobic heterotrophs that correlated with nitrification rates and N2O supersaturations, linking N2O production and accumulation to taxa involved in organic matter remineralization. Keystone taxa implicated in anaerobic carbon, nitrogen, and sulfur cycling in anoxic environments clustered together in a low-oxygen subnetwork that correlated positively with nitrification N2O yields and N2O production from denitrification. Close coupling between N2O producers and consumers in the anoxic basin is indicated by strong correlations between the low-oxygen subnetwork, PICRUSt2-predicted nitrous oxide reductase (nosZ) gene abundances, and N2O undersaturation. This study implicates keystone taxa affiliated with common ODZ groups as a potential control on water column N2O cycling and provides a theoretical basis for further investigations into marine microbial interaction networks.
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Affiliation(s)
- Brett D Jameson
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada.
| | - Sheryl A Murdock
- Department of Biology, University of Victoria, P.O. Box 1700 CSC, Victoria, BC, V8W 2Y2, Canada
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
| | - Qixing Ji
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
- Thrust of Earth, Ocean & Atmospheric Sciences, Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou, Guangdong, 511400, China
| | - Catherine J Stevens
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada
| | - Damian S Grundle
- Bermuda Institute of Ocean Sciences, 17 Biological Station, St. George's, GE01, Bermuda
- School of Ocean Futures & School of Earth & Space Exploration, Arizona State University, Tempe, AZ, 85287-7904, USA
| | - S Kim Juniper
- School of Earth & Ocean Sciences, University of Victoria, P.O. Box 1700 Station CSC, Victoria, BC, V8W 2Y2, Canada
- Department of Biology, University of Victoria, P.O. Box 1700 CSC, Victoria, BC, V8W 2Y2, Canada
- Ocean Networks Canada, 2474 Arbutus Road, Victoria, BC, V8N 1V8, Canada
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13
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Lu Y, Lv Y, Zhang Y, Liu Q, Xu X, Xiao X, Xu J. Metatranscriptomes reveal the diverse responses of Thaumarchaeota ecotypes to environmental variations in the northern slope of the South China Sea. Environ Microbiol 2023; 25:410-427. [PMID: 36448268 DOI: 10.1111/1462-2920.16289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022]
Abstract
Thaumarchaeota are among the most abundant prokaryotes in the ocean, playing important roles in carbon and nitrogen cycling. Marine Thaumarchaeota ecotypes exhibit depth-related diversification and seasonal changes. However, transcriptomic activities concerning niche partitioning among thaumarchaeal ecotypes remain unclear. Here, we examined the variations in the distribution and transcriptomic activity of marine Thaumarchaeota ecotypes. Three primary ecotypes were identified: a Nitrosopumilus-like clade; a Nitrosopelagicus-like water column A (WCA) clade, thriving in epipelagic water; and a water column B (WCB) clade, dominant in deep water. Depth-related partitioning of the three ecotypes and the seasonal variability of the WCA and WCB ecotypes were observed. Nutrient concentrations, chlorophyll α and salinity were the primary environmental factors. The relative abundance of the WCA ecotype and its transcript abundance of amoA gene were positively correlated with chlorophyll α and salinity, while the WCB ecotype was positively correlated with nitrate and phosphate. Based on high-quality metagenome-assembled genomes, transcriptomic analysis revealed that the three ecotypes exhibited various co-occurring expression patterns of the elemental cycling genes in the nitrogen, carbon, phosphorus, and sulfur cycles. Our results provide transcriptomic evidence of the niche differentiation of marine Thaumarchaeota ecotypes, highlighting the diverse roles of ecotypes and WCA subclades in biogeochemical cycles.
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Affiliation(s)
- Ye Lu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yongxin Lv
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Liu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Xuewei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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14
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Niu T, Xu Y, Chen J, Qin L, Li Z, Yang Y, Liang J. Bacterial taxonomic and functional profiles from Bohai Sea to northern Yellow Sea. Front Microbiol 2023; 14:1139950. [PMID: 36910186 PMCID: PMC9995391 DOI: 10.3389/fmicb.2023.1139950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Microbial distribution patterns are the result of a combination of biotic and abiotic factors, which are the core issues in microbial ecology research. To better understand the biogeographic pattern of bacteria in water environments from the Bohai Sea to the northern Yellow Sea, the effects of environmental factors, and spatial distance on the structure of bacterial communities in marine water were investigated using high-throughput sequencing technology based on 16S rRNA genes. The results showed that Proteobacteria, Bacteroidetes, Actinobacteri, Desulfobacterota, and Bdellovibrionota were the dominant phyla in the study area. A clear spatial pattern in the bacterial community was observed, and environmental factors, including salinity, nutrient concentration, carbon content, total phosphorus, dissolved oxygen, and seawater turbidity emerged as the central environmental factors regulating the variation in bacterial communities. In addition, the study provides direct evidence of the existence of dispersal limitation in this strongly connected marine ecological system. Therefore, these results revealed that the variation in bacterial community characteristics was attributed to environmental selection, accompanied by the regulation of stochastic diffusion. The network analysis demonstrated a nonrandom co-occurrence pattern in the microbial communities with distinct spatial distribution characteristics. It is implied that the biogeography patterns of bacterial community may also be associated with the characteristics of co-occurrence characterize among bacterial species. Furthermore, the PICRUSt analysis indicated a clear spatial distribution of functional characteristics in bacterial communities. This functional variation was significantly modulated by the environmental characteristics of seawater but uncoupled from the taxonomic characteristics of bacterial communities (e.g., diversity characteristics, community structure, and co-occurrence relationships). Together, this findings represent a significant advance in linking seawater to the mechanisms underlying bacterial biogeographic patterns and community assembly, co-occurrence patterns, and ecological functions, providing new insights for identifying the microbial ecology as well as the biogeochemical cycle in the marine environment.
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Affiliation(s)
- Tianyi Niu
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Yongqian Xu
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Jinni Chen
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Liangyun Qin
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhicong Li
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Yating Yang
- School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- School of Marine Sciences, Guangxi University, Nanning, China.,Coral Reef Research Center of China, Guangxi University, Nanning, China.,Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Nanning, China
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15
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Sun X, Zhao J, Zhang L, Zhou X, Xia W, Zhao Y, Jia Z. Effects of agricultural land use on the differentiation of nitrifier communities and functional patterns from natural terrestrial ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155568. [PMID: 35490817 DOI: 10.1016/j.scitotenv.2022.155568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/19/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Human activities severely affect the global nitrogen (N) cycle. Croplands receive intensive N fertilization; consequently, cropland and natural ecosystem differentiation often results in community and functional variation in N-transforming microbes, including nitrifiers, which perform nitrification central to N cycle. However, evidence of such variation is mostly limited to ammonia oxidizers (AO) in local fields, excluding soil heterogeneity and nitrite-oxidizing bacteria (NOB); the variation under diverse climatic and soil conditions is not comprehensively understood. We conducted a large-scale survey of 131 cropland and natural sites in China. The community patterns of ammonia-oxidizing bacteria (AOB) and NOB differed significantly between croplands and some natural ecosystems, whereas ammonia-oxidizing archaea (AOA) were not affected by ecosystem type. The AOB population and nitrification potential (NP) were significantly higher in agroecosystems than in natural systems except wetlands. Fewer co-occurrence interactions involving nitrifiers were observed in croplands than in natural ecosystems except forests, systematically indicating the ecological diversification of nitrifiers in potential microbial associations among these habitats. Ecosystem type, pH, organic matter (OM), total phosphorus (TP), mean annual temperature (MAT) and mean annual precipitation (MAP) were primary drivers of nitrifier community and functional shifts. This study provides the first large-scale evidence of overall nitrifier community (i.e., AOA, AOB and NOB) and potential functional shifts between agroecosystems and natural environments, enabling predictions of terrestrial N cycle under foreseeable natural land use conversions and global climate change.
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Affiliation(s)
- Xiangxin Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, Jiangsu Province, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Zhao
- Institute for Food and Agricultural Sciences (IFAS), Department of Microbiology & Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie 33314, FL, USA
| | - Liyan Zhang
- College of Environment, Hohai University, Nanjing 210098, Jiangsu Province, China
| | - Xue Zhou
- College of Agricultural Science and Engineering, Hohai University, Nanjing 210098, Jiangsu Province, China
| | - Weiwei Xia
- College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, Jiangsu Province, China
| | - Yuguo Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, Jiangsu Province, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, Jiangsu Province, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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16
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Thiele S, Storesund JE, Fernández-Méndez M, Assmy P, Øvreås L. A Winter-to-Summer Transition of Bacterial and Archaeal Communities in Arctic Sea Ice. Microorganisms 2022; 10:1618. [PMID: 36014036 PMCID: PMC9414599 DOI: 10.3390/microorganisms10081618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
The Arctic is warming 2-3 times faster than the global average, leading to a decrease in Arctic sea ice extent, thickness, and associated changes in sea ice structure. These changes impact sea ice habitat properties and the ice-associated ecosystems. Sea-ice algal blooms provide various algal-derived carbon sources for the bacterial and archaeal communities within the sea ice. Here, we detail the transition of these communities from winter through spring to early summer during the Norwegian young sea ICE (N-ICE2015) expedition. The winter community was dominated by the archaeon Candidatus Nitrosopumilus and bacteria belonging to the Gammaproteobacteria (Colwellia, Kangiellaceae, and Nitrinocolaceae), indicating that nitrogen-based metabolisms, particularly ammonia oxidation to nitrite by Cand. Nitrosopumilus was prevalent. At the onset of the vernal sea-ice algae bloom, the community shifted to the dominance of Gammaproteobacteria (Kangiellaceae, Nitrinocolaceae) and Bacteroidia (Polaribacter), while Cand. Nitrosopumilus almost disappeared. The bioinformatically predicted carbohydrate-active enzymes increased during spring and summer, indicating that sea-ice algae-derived carbon sources are a strong driver of bacterial and archaeal community succession in Arctic sea ice during the change of seasons. This implies a succession from a nitrogen metabolism-based winter community to an algal-derived carbon metabolism-based spring/ summer community.
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Affiliation(s)
- Stefan Thiele
- Department of Biological Science, University of Bergen, Thormøhlensgate 53 A/B, 5020 Bergen, Norway
- Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
| | | | - Mar Fernández-Méndez
- Norwegian Polar Institute, Fram Centre, Hjalmar Johansens Gate 14, 9296 Tromsø, Norway
- Biological Oceanography, GEOMAR Helmholtz Centre of Ocean Research, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Philipp Assmy
- Norwegian Polar Institute, Fram Centre, Hjalmar Johansens Gate 14, 9296 Tromsø, Norway
| | - Lise Øvreås
- Department of Biological Science, University of Bergen, Thormøhlensgate 53 A/B, 5020 Bergen, Norway
- Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway
- Department of Arctic Biology, University Center in Svalbard, UNIS, 9171 Longyearbyen, Norway
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Dynamics of actively dividing prokaryotes in the western Mediterranean Sea. Sci Rep 2022; 12:2064. [PMID: 35136122 PMCID: PMC8825817 DOI: 10.1038/s41598-022-06120-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 01/25/2022] [Indexed: 11/29/2022] Open
Abstract
Microbial community metabolism and functionality play a key role modulating global biogeochemical processes. However, the metabolic activities and contribution of actively growing prokaryotes to ecosystem energy fluxes remain underexplored. Here we describe the temporal and spatial dynamics of active prokaryotes in the different water masses of the Mediterranean Sea using a combination of bromodeoxyuridine labelling and 16S rRNA gene Illumina sequencing. Bulk and actively dividing prokaryotic communities were drastically different and depth stratified. Alteromonadales were rare in bulk communities (contributing 0.1% on average) but dominated the actively dividing community throughout the overall water column (28% on average). Moreover, temporal variability of actively dividing Alteromonadales oligotypes was evinced. SAR86, Actinomarinales and Rhodobacterales contributed on average 3–3.4% each to the bulk and 11, 8.4 and 8.5% to the actively dividing communities in the epipelagic zone, respectively. SAR11 and Nitrosopumilales contributed less to the actively dividing than to the bulk communities during all the study period. Noticeably, the large contribution of these two taxa to the total prokaryotic communities (23% SAR11 and 26% Nitrosopumilales), especially in the meso- and bathypelagic zones, results in important contributions to actively dividing communities (11% SAR11 and 12% Nitrosopumilales). The intense temporal and spatial variability of actively dividing communities revealed in this study strengthen the view of a highly dynamic deep ocean. Our results suggest that some rare or low abundant phylotypes from surface layers down to the deep sea can disproportionally contribute to the activity of the prokaryotic communities, exhibiting a more dynamic response to environmental changes than other abundant phylotypes, emphasizing the role they might have in community metabolism and biogeochemical processes.
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Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay. mSystems 2022; 7:e0127021. [PMID: 35076275 PMCID: PMC8788347 DOI: 10.1128/msystems.01270-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) are key for the transformation of ammonia to oxidized forms of nitrogen in aquatic environments around the globe, including nutrient-rich coastal and estuarine waters such as San Francisco Bay (SFB). Using metagenomics and 16S rRNA gene amplicon libraries, we found that AOA are more abundant than ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), except in the freshwater stations in SFB. In South SFB, we observed recurrent AOA blooms of “Candidatus Nitrosomarinus catalina” SPOT01-like organisms, which account for over 20% of 16S rRNA gene amplicons in both surface and bottom waters and co-occur with weeks of high nitrite concentrations (>10 μM) in the oxic water column. We observed pronounced nitrite peaks occurring in the autumn for 7 of the last 9 years (2012 to 2020), suggesting that seasonal AOA blooms are common in South SFB. We recovered two high-quality AOA metagenome-assembled genomes (MAGs), including a Nitrosomarinus-like genome from the South SFB bloom and another Nitrosopumilus genome originating from Suisun Bay in North SFB. Both MAGs cluster with genomes from other estuarine/coastal sites. Analysis of Nitrosomarinus-like genomes show that they are streamlined, with low GC content and high coding density, and harbor urease genes. Our findings support the unique niche of Nitrosomarinus-like organisms which dominate coastal/estuarine waters and provide insights into recurring AOA blooms in SFB. IMPORTANCE Ammonia-oxidizing archaea (AOA) carry out key transformations of ammonia in estuarine systems such as San Francisco Bay (SFB)—the largest estuary on the west coast of North America—and play a significant role in both local and global nitrogen cycling. Using metagenomics and 16S rRNA gene amplicon libraries, we document a massive, recurrent AOA bloom in South SFB that co-occurs with months of high nitrite concentrations in the oxic water column. Our study is the first to generate metagenome-assembled genomes (MAGs) from SFB, and through this process we recovered two high-quality AOA MAGs, one of which originated from bloom samples. These AOA MAGs yield new insight into the Nitrosopumilus and Nitrosomarinus-like lineages and their potential niches in coastal and estuarine systems. Nitrosomarinus-like AOA are abundant in coastal regions around the globe, and we highlight the common occurrence of urease genes, low GC content, and range of salinity tolerances within this lineage.
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He T, Xu ZJ, Wang JF, Wang FP, Zhou XF, Wang LL, Li QS. Improving cadmium accumulation by Solanum nigrum L. via regulating rhizobacterial community and metabolic function with phosphate-solubilizing bacteria colonization. CHEMOSPHERE 2022; 287:132209. [PMID: 34826911 DOI: 10.1016/j.chemosphere.2021.132209] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 05/03/2023]
Abstract
Soil cadmium (Cd) mobilized with phosphate-solubilizing bacteria (PSB), especially for strains effectively colonized in rhizosphere, is an important pathway for promoting its accumulation by Cd-hyperaccumulators. In this study, screened PSB strains, Acinetobacter pittii (AP) and Escherichia coli (EC), were used to evaluate their effects on Cd mobilization in rhizosphere, Cd accumulation by Solanum nigrum L., and rhizobacterial community and metabolic function under different colonization condition. Results indicated that AP or EC inoculated in soils significantly promoted plant growth, and simultaneously motivated Cd accumulation in S. nigrum L. by 119% and 88%, respectively, when compared with that of uninoculated treatment. Higher efficiency colonization of AP contributed to more organic acids (malic, l-proline, l-alanine, and γ-aminobutanoic) production in the rhizosphere soil and Cd accumulation by S. nigrum L., when compared with that of EC treatment. Taxonomic distribution and co-occurrence network analyses demonstrated that inoculation of AP or EC enriched dominant microbial taxa with plant growth promotion function and keystone taxa related to Cd mobilization in the rhizosphere soil, respectively. Inoculated strains up-regulated the expression of genes related to bacterial mobility, amino acid metabolism, and carbon metabolism among rhizobacterial community. Overall, this study provided a feasible method for soil Cd phytoremediation by promoting Cd mobilization with the enhancement of keystone taxa and organic acid secretion based on the high-efficiency colonization of PSB.
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Affiliation(s)
- Tao He
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Zi-Jie Xu
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Jun-Feng Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Fo-Peng Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Xue-Fang Zhou
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Li-Li Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Qu-Sheng Li
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China.
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20
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Wang S, Hou W, Jiang H, Dong H, Huang L, Chen S, Wang B, Chen Y, Lin B, Deng Y. The Lifestyle-Dependent Microbial Interactions Vary Between Upstream and Downstream of the Three Gorges Dam. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.624476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Dams represent the most significant anthropogenic disturbance to global rivers. Previous studies have shown that free-living and particle-attached microbes exhibited differentially in river and reservoir ecosystems. However, little is known about the dam’s effect on their co-occurrence patterns. Here, a random matrix theory (RMT)-based network approach was used to construct microbial ecological networks for free-living and particle-attached communities in the immediate vicinity of the Three Gorges Dam (TGD), based on a high-throughput sequencing of 16S rRNA gene. Microbial distribution pattern showed that differences caused by lifestyle (free-living vs. particle-attached) were greater than those caused by geographic position (upstream vs. downstream of the TGD). Network analysis revealed higher connectivity and a lower number of modules in the overall downstream networks. Furthermore, considering the lifestyle, the network structures and properties for free-living and particle-attached microbes were different between upstream and downstream of the dam. Specifically, free-living communities located upstream of the dam exhibited a more complex co-occurrence pattern than the particle-attached communities, whereas the opposite was true for those located downstream of the dam. This variation indicated a strong impact of the dam on microbial interactions for microbes with similar lifestyle in the vicinity of the dam. We identified 112 persistent operational taxonomic unit (OTU)-level species that stably coexisted regardless of lifestyle and geographic positions. These persistent species occupied 21.33–25.57% of the total nodes in each network, and together with their first neighbors, they contributed more than 50% of the nodes and edges belonging to each network. Furthermore, we found that taxonomic affiliations for central nodes (with high degree) varied in these persistent species sub-networks. Collectively, our findings expand the current understanding of the dam’s effect on species interaction variation patterns for free-living and particle-attached communities in the vicinity of the dam, which are more complex than traditional alpha and beta microbial diversity.
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21
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Stephens BM, Opalk K, Petras D, Liu S, Comstock J, Aluwihare LI, Hansell DA, Carlson CA. Organic Matter Composition at Ocean Station Papa Affects Its Bioavailability, Bacterioplankton Growth Efficiency and the Responding Taxa. FRONTIERS IN MARINE SCIENCE 2021; 2021:10.3389/fmars.2020.590273. [PMID: 35004707 PMCID: PMC8740527 DOI: 10.3389/fmars.2020.590273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The bioavailability of organic matter (OM) to marine heterotrophic bacterioplankton is determined by both the chemical composition of OM and the microbial community composition. In the current study, changes in OM bioavailability were identified at Ocean Station Papa as part of the 2018 Export Processes in the Ocean from Remote Sensing (EXPORTS) field study. Removal rates of carbon (C) in controlled experiments were significantly correlated with the initial composition of total hydrolyzable amino acids, and C removal rates were high when the amino acid degradation index suggested a more labile composition. Carbon remineralization rates averaged 0.19 ± 0.08 μmol C L-1 d-1 over 6-10 days while bacterial growth efficiencies averaged 31 ± 7%. Amino acid composition and tandem mass spectrometry analysis of compound classes also revealed transformations to a more degraded OM composition during experiments. There was a log2-fold increase in the relative abundances of 16S rDNA-resolved bacterioplankton taxa in most experiments by members of the Methylophilaceae family (OM43 genus) and KI89A order. Additionally, when OM was more bioavailable, relative abundances increased by at least threefold for the classes Bacteroidetes (Flavobacteriaceae NS2b genus), Alphaproteobacteria (Rhodobacteraceae Sulfitobacter genus), and Gammaproteobacteria (Alteromonadales and Ectothiorhodospiraceae orders). Our data suggest that a diverse group of bacterioplankton was responsible for removing organic carbon and altering the OM composition to a more degraded state. Elevated community diversity, as inferred from the Shannon-Wiener H index, may have contributed to relatively high growth efficiencies by the bacterioplankton. The data presented here shed light on the interconnections between OM bioavailability and key bacterioplankton taxa for the degradation of marine OM.
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Affiliation(s)
- Brandon M. Stephens
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Keri Opalk
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Shuting Liu
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Jacqueline Comstock
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Lihini I. Aluwihare
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Dennis A. Hansell
- Department of Ocean Sciences, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Miami, FL, United States
| | - Craig A. Carlson
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
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22
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Kusch S, Wakeham SG, Dildar N, Zhu C, Sepúlveda J. Bacterial and archaeal lipids trace chemo(auto)trophy along the redoxcline in Vancouver Island fjords. GEOBIOLOGY 2021; 19:521-541. [PMID: 33960615 DOI: 10.1111/gbi.12446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/30/2021] [Accepted: 04/10/2021] [Indexed: 11/29/2022]
Abstract
Marine oxygen minimum zones play a crucial role in the global oceanic carbon, nitrogen, and sulfur cycles as they harbor microbial communities that are adapted to the water column chemistry and redox zonation, and in turn control the water column chemistry and greenhouse gas release. These micro-organisms have metabolisms that rely on terminal electron acceptors other than O2 and often benefit from syntrophic relationships (metabolic coupling). Here, we study chemo(auto)trophy along the redoxcline in two stratified fjords on Vancouver Island (Canada) using bacterial bacteriohopanepolyols and archaeal ether lipids. We analyze the distribution of these lipid classes in suspended particulate matter (SPM) to trace ammonia oxidation, anaerobic ammonium oxidation (anammox), sulfate reduction/sulfur oxidation, methanogenesis, and methane oxidation, and investigate ecological niches to evaluate potential links between their respective bacterial and archaeal sources. Our results show an unparalleled BHP and ether lipid structural diversity that allows tracing the major redox-driven metabolic processes at the time of sampling: Both fjords are dominated by archaeal ammonia oxidation and anammox; sulfate-reducing bacteria may be present in Deer Bay, but absent from Effingham Inlet; methanogenic Euryarchaeota and archaeal and bacterial methanotrophs are detectable at low abundance. Correlation analysis reveals distinct biomarker clusters that provide constraints on the biogeochemical niches of some orphan BHP and ether lipids such as in situ-produced adenosyl-BHPs or unsaturated archaeols.
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Affiliation(s)
- Stephanie Kusch
- University of Cologne Centre for Accelerator Mass Spectrometry, University of Cologne, Cologne, Germany
| | - Stuart G Wakeham
- Skidaway Institute of Oceanography, University of Georgia, Savannah, GA, USA
| | - Nadia Dildar
- Department of Geological Sciences and Institute of Arctic and Alpine Research (INSTAAR), University of Colorado Boulder, Boulder, CO, USA
| | - Chun Zhu
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Julio Sepúlveda
- Department of Geological Sciences and Institute of Arctic and Alpine Research (INSTAAR), University of Colorado Boulder, Boulder, CO, USA
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23
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Gaiero JR, Tosi M, Bent E, Boitt G, Khosla K, Turner BL, Richardson AE, Condron LM, Dunfield KE. Soil microbial communities influencing organic phosphorus mineralization in a coastal dune chronosequence in New Zealand. FEMS Microbiol Ecol 2021; 97:6145523. [PMID: 33609120 DOI: 10.1093/femsec/fiab034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/18/2021] [Indexed: 01/04/2023] Open
Abstract
The Haast chronosequence in New Zealand is an ∼6500-year dune formation series, characterized by rapid podzol development, phosphorus (P) depletion and a decline in aboveground biomass. We examined bacterial and fungal community composition within mineral soil fractions using amplicon-based high-throughput sequencing (Illumina MiSeq). We targeted bacterial non-specific acid (class A, phoN/phoC) and alkaline (phoD) phosphomonoesterase genes and quantified specific genes and transcripts using real-time PCR. Soil bacterial diversity was greatest after 4000 years of ecosystem development and associated with an increased richness of phylotypes and a significant decline in previously dominant taxa (Firmicutes and Proteobacteria). Soil fungal communities transitioned from predominantly Basidiomycota to Ascomycota along the chronosequence and were most diverse in 290- to 392-year-old soils, coinciding with maximum tree basal area and organic P accumulation. The Bacteria:Fungi ratio decreased amid a competitive and interconnected soil community as determined by network analysis. Overall, soil microbial communities were associated with soil changes and declining P throughout pedogenesis and ecosystem succession. We identified an increased dependence on organic P mineralization, as found by the profiled acid phosphatase genes, soil acid phosphatase activity and function inference from predicted metagenomes (PICRUSt2).
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Affiliation(s)
- Jonathan R Gaiero
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Micaela Tosi
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Elizabeth Bent
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Gustavo Boitt
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Kamini Khosla
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Benjamin L Turner
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, Republic of Panama
| | | | - Leo M Condron
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, Canterbury, New Zealand
| | - Kari E Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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24
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Lewis WH, Tahon G, Geesink P, Sousa DZ, Ettema TJG. Innovations to culturing the uncultured microbial majority. Nat Rev Microbiol 2021; 19:225-240. [PMID: 33093661 DOI: 10.1038/s41579-020-00458-8] [Citation(s) in RCA: 200] [Impact Index Per Article: 66.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2020] [Indexed: 02/07/2023]
Abstract
Despite the surge of microbial genome data, experimental testing is important to confirm inferences about the cell biology, ecological roles and evolution of microorganisms. As the majority of archaeal and bacterial diversity remains uncultured and poorly characterized, culturing is a priority. The growing interest in and need for efficient cultivation strategies has led to many rapid methodological and technological advances. In this Review, we discuss common barriers that can hamper the isolation and culturing of novel microorganisms and review emerging, innovative methods for targeted or high-throughput cultivation. We also highlight recent examples of successful cultivation of novel archaea and bacteria, and suggest key microorganisms for future cultivation attempts.
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Affiliation(s)
- William H Lewis
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Guillaume Tahon
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Patricia Geesink
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
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25
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Shafiee RT, Diver PJ, Snow JT, Zhang Q, Rickaby REM. Marine ammonia-oxidising archaea and bacteria occupy distinct iron and copper niches. ISME COMMUNICATIONS 2021; 1:1. [PMID: 37938628 PMCID: PMC9723733 DOI: 10.1038/s43705-021-00001-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/11/2020] [Accepted: 01/06/2021] [Indexed: 12/22/2022]
Abstract
Ammonia oxidation by archaea and bacteria (AOA and AOB), is the first step of nitrification in the oceans. As AOA have an ammonium affinity 200-fold higher than AOB isolates, the chemical niche allowing AOB to persist in the oligotrophic ocean remains unclear. Here we show that marine isolates, Nitrosopumilus maritimus strain SCM1 (AOA) and Nitrosococcus oceani strain C-107 (AOB) have contrasting physiologies in response to the trace metals iron (Fe) and copper (Cu), holding potential implications for their niche separation in the oceans. A greater affinity for unchelated Fe may allow AOB to inhabit shallower, euphotic waters where ammonium supply is high, but competition for Fe is rife. In contrast to AOB, AOA isolates have a greater affinity and toxicity threshold for unchelated Cu providing additional explanation to the greater success of AOA in the marine environment where Cu availability can be highly variable. Using comparative genomics, we predict that the proteomic and metal transport basis giving rise to contrasting physiologies in isolates is widespread across phylogenetically diverse marine AOA and AOB that are not yet available in pure culture. Our results develop the testable hypothesis that ammonia oxidation may be limited by Cu in large tracts of the open ocean and suggest a relatively earlier emergence of AOB than AOA when considered in the context of evolving trace metal availabilities over geologic time.
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Affiliation(s)
- Roxana T Shafiee
- Department of Earth Sciences, University of Oxford, Oxfordshire, UK.
| | - Poppy J Diver
- Department of Earth Sciences, University of Oxford, Oxfordshire, UK
| | - Joseph T Snow
- Department of Earth Sciences, University of Oxford, Oxfordshire, UK
| | - Qiong Zhang
- Department of Earth Sciences, University of Oxford, Oxfordshire, UK
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26
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Ammonia-oxidizing archaea in biological interactions. J Microbiol 2021; 59:298-310. [DOI: 10.1007/s12275-021-1005-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 10/22/2022]
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27
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Huang Y, Xu D, Huang LY, Lou YT, Muhadesi JB, Qian HC, Zhou EZ, Wang BJ, Li XT, Jiang Z, Liu SJ, Zhang DW, Jiang CY. Responses of soil microbiome to steel corrosion. NPJ Biofilms Microbiomes 2021; 7:6. [PMID: 33479252 PMCID: PMC7820017 DOI: 10.1038/s41522-020-00175-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/24/2020] [Indexed: 11/09/2022] Open
Abstract
The process of microbiologically influenced corrosion (MIC) in soils has received widespread attention. Herein, long-term outdoor soil burial experiments were conducted to elucidate the community composition and functional interaction of soil microorganisms associated with metal corrosion. The results indicated that iron-oxidizing (e.g., Gallionella), nitrifying (e.g., Nitrospira), and denitrifying (e.g., Hydrogenophaga) microorganisms were significantly enriched in response to metal corrosion and were positively correlated with the metal mass loss. Corrosion process may promote the preferential growth of the abundant microbes. The functional annotation revealed that the metabolic processes of nitrogen cycling and electron transfer pathways were strengthened, and also that the corrosion of metals in soil was closely associated with the biogeochemical cycling of iron and nitrogen elements and extracellular electron transfer. Niche disturbance of microbial communities induced by the buried metals facilitated the synergetic effect of the major MIC participants. The co-occurrence network analysis suggested possible niche correlations among corrosion related bioindicators.
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Affiliation(s)
- Ye Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dake Xu
- Shenyang National Laboratory for Material Sciences, Northeastern University, Shenyang, 110819, China
| | - Lu-Yao Huang
- Beijing Advanced Innovation Center for Materials Genome Engineering, National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yun-Tian Lou
- Beijing Advanced Innovation Center for Materials Genome Engineering, National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, 100083, China
| | - Jiang-Baota Muhadesi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Chang Qian
- Beijing Advanced Innovation Center for Materials Genome Engineering, National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, 100083, China
| | - En-Ze Zhou
- Shenyang National Laboratory for Material Sciences, Northeastern University, Shenyang, 110819, China
| | - Bao-Jun Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiu-Tong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Da-Wei Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, National Materials Corrosion and Protection Data Center, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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28
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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.
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29
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Wu G, Ge L, Zhao N, Liu F, Shi Z, Zheng N, Zhou D, Jiang X, Halverson L, Xie B. Environment dependent microbial co-occurrences across a cyanobacterial bloom in a freshwater lake. Environ Microbiol 2020; 23:327-339. [PMID: 33185973 DOI: 10.1111/1462-2920.15315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/28/2020] [Accepted: 11/09/2020] [Indexed: 11/29/2022]
Abstract
Microbial taxon-taxon co-occurrences may directly or indirectly reflect the potential relationships between the members within a microbial community. However, to what extent and the specificity by which these co-occurrences are influenced by environmental factors remains unclear. In this report, we evaluated how the dynamics of microbial taxon-taxon co-occurrence is associated with the changes of environmental factors in Nan Lake at Wuhan city, China with a Modified Liquid Association method. We were able to detect more than 1000 taxon-taxon co-occurrences highly correlated with one or more environmental factors across a phytoplankton bloom using 16S rRNA gene amplicon community profiles. These co-occurrences, referred to as environment dependent co-occurrences (ED_co-occurrences), delineate a unique network in which a taxon-taxon pair exhibits specific, and potentially dynamic correlations with an environmental parameter, while the individual relative abundance of each may not. Microcystis involved ED_co-occurrences are in important topological positions in the network, suggesting relationships between the bloom dominant species and other taxa could play a role in the interplay of microbial community and environment across various bloom stages. Our results may broaden our understanding of the response of a microbial community to the environment, particularly at the level of microbe-microbe associations.
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Affiliation(s)
- Gang Wu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China
| | - Leixin Ge
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China
| | - Na Zhao
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China
| | - Fei Liu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China
| | - Zunji Shi
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China
| | - Ningning Zheng
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China
| | - Dan Zhou
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China.,School of Biological Sciences, Guizhou Normal College, Guiyang, Guizhou, 550018, China
| | - Xingpeng Jiang
- School of Computer, Central China Normal University, Wuhan, 430079, China
| | - Larry Halverson
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Bo Xie
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, 430079, China
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30
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Dai J, Ye Q, Wu Y, Zhang M, Zhang J. Simulation of Enhanced Growth of Marine Group II Euryarchaeota From the Deep Chlorophyll Maximum of the Western Pacific Ocean: Implication for Upwelling Impact on Microbial Functions in the Photic Zone. Front Microbiol 2020; 11:571199. [PMID: 33013804 PMCID: PMC7516215 DOI: 10.3389/fmicb.2020.571199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/13/2020] [Indexed: 11/13/2022] Open
Abstract
Mesoscale eddies can have a strong impact on regional biogeochemistry and primary productivity. To investigate the effect of the upwelling of seawater by western Pacific eddies on the composition of the active planktonic marine archaeal community composition of the deep chlorophyll maximum (DCM) layer, mesoscale cold-core eddies were simulated in situ by mixing western Pacific DCM layer water with mesopelagic layer (400 m) water. Illumina sequencing of the 16S rRNA gene and 16S rRNA transcripts indicated that the specific heterotrophic Marine Group IIb (MGIIb) taxonomic group of the DCM layer was rapidly stimulated after receiving fresh substrate from 400 m water, which was dominated by uncultured autotrophic Marine Group I (MGI) archaea. Furthermore, niche differentiation of autotrophic ammonia-oxidizing archaea (MGI) was demonstrated by deep sequencing of 16S rRNA, amoA, and accA genes, respectively. Similar distribution patterns of active Marine Group III (MGIII) were observed in the DCM layer with or without vertical mixing, indicating that they are inclined to utilize the substrates already present in the DCM layer. These findings underscore the importance of mesoscale cyclonic eddies in stimulating microbial processes involved in the regional carbon cycle.
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Affiliation(s)
- Jinlong Dai
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Qi Ye
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Ying Wu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Miao Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Jing Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
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31
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Liu R, Wang Z, Wang L, Li Z, Fang J, Wei X, Wei W, Cao J, Wei Y, Xie Z. Bulk and Active Sediment Prokaryotic Communities in the Mariana and Mussau Trenches. Front Microbiol 2020; 11:1521. [PMID: 32765444 PMCID: PMC7381213 DOI: 10.3389/fmicb.2020.01521] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 06/11/2020] [Indexed: 12/19/2022] Open
Abstract
Surprisingly high rates of microbial respiration have recently been reported in hadal trench sediment, yet the potentially active microorganisms and specific microbe–microbe relationships in trench sediment are largely unknown. We investigated the bulk and active prokaryotic communities and co-occurrence interactions of different lineages in vertically sectioned sediment cores taken from the deepest points of the Mariana and Mussau Trenches. Analysis on species novelty revealed for the first time the high rate of novel lineages in the microbial communities of the hadal trenches. Using 95, 97, and 99% similarity as thresholds, averagely 22.29, 32.3, and 64.1% of total OTUs retrieved from sediments of the two trenches were identified as the potentially novel lineages, respectively. The compositions of the potentially active communities, revealed via ribosomal RNA (rRNA), were significantly different from those of bulk communities (rDNA) in all samples from both trenches. The dominant taxa in bulk communities generally accounted for low proportions in the rRNA libraries, signifying that the abundance was not necessarily related to community functions in the hadal sediments. The potentially active communities showed high diversity and composed primarily of heterotrophic lineages, supporting their potential contributions in organic carbon consumption. Network analysis revealed high modularity and non-random co-occurrence of phylogenetically unrelated taxa, indicating highly specified micro-niches and close microbial interactions in the hadal sediments tested. Combined analysis of activity potentials and network keystone scores revealed significance of phyla Chloroflexi and Gemmatimonadetes, as well as several potentially alkane-degrading taxa in maintaining microbial interactions and functions of the trench communities. Overall, our results demonstrate that the hadal trenches harbor diverse, closely interacting, and active microorganisms, despite the extreme environmental conditions.
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Affiliation(s)
- Rulong Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Zixuan Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Li Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Zhenzhen Li
- State Key Laboratory of Geological Processes and Mineral Resources, Department of Earth Sciences, China University of Geosciences, Wuhan, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Department of Natural Science, Hawaii Pacific University, Honolulu, HI, United States
| | - Xing Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Wenxia Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Yuli Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Zhe Xie
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
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32
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Reji L, Tolar BB, Chavez FP, Francis CA. Depth-Differentiation and Seasonality of Planktonic Microbial Assemblages in the Monterey Bay Upwelling System. Front Microbiol 2020; 11:1075. [PMID: 32523584 PMCID: PMC7261934 DOI: 10.3389/fmicb.2020.01075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/29/2020] [Indexed: 11/23/2022] Open
Abstract
Coastal upwelling regions are hotspots of biological productivity, supporting diverse communities of microbial life and metabolisms. Monterey Bay (MB), a coastal ocean embayment in central California, experiences seasonal upwelling of cold, nutrient-rich waters that sustain episodes of high phytoplankton production in surface waters. While productivity in surface waters is intimately linked to metabolisms of diverse communities of Archaea and Bacteria, a comprehensive understanding of the microbial community in MB is missing thus far, particularly in relation to the distinct hydrographic seasons characteristic of the MB system. Here we present the results of a 2-year microbial time-series survey in MB, investigating community composition and structure across spatiotemporal gradients. In deciphering these patterns, we used unique sequence variants (SVs) of the 16S rRNA gene (V4–V5 region), complemented with metagenomes and metatranscriptomes representing multiple depth profiles. We found clear depth-differentiation and recurring seasonal abundance patterns within planktonic communities, particularly when analyzed at finer taxonomic levels. Compositional changes were more pronounced in the upper 0–40 m of the water column, whereas deeper depths were characterized by temporally stable populations. In accordance with the dynamic nutrient profiles, the system appears to change from a Bacteroidetes- and Rhodobacterales-dominated upwelling period to an oceanic season dominated by oligotrophic groups such as SAR11 and picocyanobacteria. The cascade of environmental changes brought about by upwelling and relaxation events thus impacts microbial community structure in the bay, with important implications for the temporal variability of nutrient and energy fluxes within the MB ecosystem. Our observations emphasize the need for continued monitoring of planktonic microbial communities in order to predict and manage the behavior of this sensitive marine sanctuary ecosystem, over projected intensification of upwelling in the region.
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Affiliation(s)
- Linta Reji
- Department of Earth System Science, Stanford University, Stanford, CA, United States
| | - Bradley B Tolar
- Department of Earth System Science, Stanford University, Stanford, CA, United States
| | - Francisco P Chavez
- Biological Oceanography Group, Monterey Bay Aquarium Research Institute, Moss Landing, CA, United States
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, Stanford, CA, United States
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Reji L, Francis CA. Metagenome-assembled genomes reveal unique metabolic adaptations of a basal marine Thaumarchaeota lineage. ISME JOURNAL 2020; 14:2105-2115. [PMID: 32405026 DOI: 10.1038/s41396-020-0675-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/29/2020] [Accepted: 04/29/2020] [Indexed: 12/18/2022]
Abstract
Thaumarchaeota constitute an abundant and ubiquitous phylum of Archaea that play critical roles in the global nitrogen and carbon cycles. Most well-characterized members of the phylum are chemolithoautotrophic ammonia-oxidizing archaea (AOA), which comprise up to 5 and 20% of the total single-celled life in soil and marine systems, respectively. Using two high-quality metagenome-assembled genomes (MAGs), here we describe a divergent marine thaumarchaeal clade that is devoid of the ammonia-oxidation machinery and the AOA-specific carbon-fixation pathway. Phylogenomic analyses placed these genomes within the uncultivated and largely understudied marine pSL12-like thaumarchaeal clade. The predominant mode of nutrient acquisition appears to be aerobic heterotrophy, evidenced by the presence of respiratory complexes and various organic carbon degradation pathways. Both genomes encoded several pyrroloquinoline quinone (PQQ)-dependent alcohol dehydrogenases, as well as a form III RuBisCO. Metabolic reconstructions suggest anaplerotic CO2 assimilation mediated by RuBisCO, which may be linked to the central carbon metabolism. We conclude that these genomes represent a hitherto unrecognized evolutionary link between predominantly anaerobic basal thaumarchaeal lineages and mesophilic marine AOA, with important implications for diversification within the phylum Thaumarchaeota.
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Affiliation(s)
- Linta Reji
- Earth System Science, Stanford University, Stanford, CA, USA
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34
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Huang L, Bai J, Wen X, Zhang G, Zhang C, Cui B, Liu X. Microbial resistance and resilience in response to environmental changes under the higher intensity of human activities than global average level. GLOBAL CHANGE BIOLOGY 2020; 26:2377-2389. [PMID: 31943531 DOI: 10.1111/gcb.14995] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/20/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Abstract
With the increasing intensity of global human activities, the ecosystem function, which is supported by the microbial community, will be dramatically changed and impaired. To investigate microbial resistance and resilience of microbial communities to human activities, we chose two typical types of human disturbances, urbanization, and reclamation under the higher intensity of human activities than the global average level. We examined microbial traits, including the abundance, diversity, phylogeny, and co-occurrence interactions in soil microbial communities, together with the nitrification activities observed in the subtropical coastal ecosystem of the Pearl River Estuary and in soil microcosm experiments. Microbial communities were less resistant to the environmental changes caused by urbanization than to those caused by reclamation, which was significantly reflected in the nitrogen and/or carbon-related patterns. However, most of the microbial traits could be recovered almost to the original level without significant differences in the microcosm after 40 days of incubation. The co-occurrence interactions between nitrifiers and other microbial communities were dramatically changed and could not be completely recovered, but this change did not affect their nitrification activities for balancing the ammonium in the soil to the original level during the recovery stage, suggesting that the interactions between microbial communities might have fewer effects on their activities than previously thought. This study quantitatively demonstrated that microbial communities as a whole can recover to a status similar to the original state in a short time after the removal of stress at a large ecosystem scale even under the higher intensity of human activities than global average level in coastal ecosystems, which implied a strong recovery capacity of soil microbial community even after intense human disturbance.
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Affiliation(s)
- Laibin Huang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Xiaojun Wen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Chengdong Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Baoshan Cui
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Xinhui Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
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35
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Levy M, Bassis CM, Kennedy E, Yoest KE, Becker JB, Bell J, Berger MB, Bruns TM. The rodent vaginal microbiome across the estrous cycle and the effect of genital nerve electrical stimulation. PLoS One 2020; 15:e0230170. [PMID: 32163469 PMCID: PMC7067422 DOI: 10.1371/journal.pone.0230170] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/27/2020] [Indexed: 12/12/2022] Open
Abstract
Treatment options are limited for the approximately 40% of postmenopausal women worldwide who suffer from female sexual dysfunction (FSD). Neural stimulation has shown potential as a treatment for genital arousal FSD, however the mechanisms for its improvement are unknown. One potential cause of some cases of genital arousal FSD are changes to the composition of the vaginal microbiota, which is associated with vulvovaginal atrophy. The primary hypothesis of this study was that neural stimulation may induce healthy changes in the vaginal microbiome, thereby improving genital arousal FSD symptoms. In this study we used healthy rats, which are a common animal model for sexual function, however the rat vaginal microbiome is understudied. Thus this study also sought to examine the composition of the rat vaginal microbiota. Treatment rats (n = 5) received 30 minutes of cutaneous electrical stimulation targeting the genital branch of the pudendal nerve, and Control animals (n = 4) had 30-minute sessions without stimulation. Vaginal lavage samples were taken during a 14-day baseline period including multiple estrous periods and after twice-weekly 30-minute sessions across a six-week trial period. Analysis of 16S rRNA gene sequences was used to characterize the rat vaginal microbiota in baseline samples and determine the effect of stimulation. We found that the rat vaginal microbiota is dominated by Proteobacteria, Firmicutes, and Actinobacteria, which changed in relative abundance during the estrous cycle and in relationship to each other. While the overall stimulation effects were unclear in these healthy rats, some Treatment animals had less alteration in microbiota composition between sequential samples than Control animals, suggesting that stimulation may help stabilize the vaginal microbiome. Future studies may consider additional physiological parameters, in addition to the microbiome composition, to further examine vaginal health and the effects of stimulation.
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Affiliation(s)
- Micah Levy
- Neuroscience, University of Michigan, Ann Arbor, Michigan, United States of America
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Christine M. Bassis
- Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Eric Kennedy
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Katie E. Yoest
- Psychology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jill B. Becker
- Psychology, University of Michigan, Ann Arbor, Michigan, United States of America
- Molecular and Behavioral Neurosciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jason Bell
- Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Mitchell B. Berger
- Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, United States of America
- Obstetrics and Gynecology, Main Line Health, Wynnewood, Pennsylvania, United States of America
| | - Tim M. Bruns
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
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36
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Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean. Nat Commun 2020; 11:767. [PMID: 32034151 PMCID: PMC7005884 DOI: 10.1038/s41467-020-14542-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 01/17/2020] [Indexed: 11/11/2022] Open
Abstract
Nitrification, the oxidation of ammonia via nitrite to nitrate, is a key process in marine nitrogen (N) cycling. Although oceanic ammonia and nitrite oxidation are balanced, ammonia-oxidizing archaea (AOA) vastly outnumber the main nitrite oxidizers, the bacterial Nitrospinae. The ecophysiological reasons for this discrepancy in abundance are unclear. Here, we compare substrate utilization and growth of Nitrospinae to AOA in the Gulf of Mexico. Based on our results, more than half of the Nitrospinae cellular N-demand is met by the organic-N compounds urea and cyanate, while AOA mainly assimilate ammonium. Nitrospinae have, under in situ conditions, around four-times higher biomass yield and five-times higher growth rates than AOA, despite their ten-fold lower abundance. Our combined results indicate that differences in mortality between Nitrospinae and AOA, rather than thermodynamics, biomass yield and cell size, determine the abundances of these main marine nitrifiers. Furthermore, there is no need to invoke yet undiscovered, abundant nitrite oxidizers to explain nitrification rates in the ocean. Ammonia oxidizing archaea and Nitrospinae are the main known nitrifiers in the ocean, but the much greater abundance of the former is puzzling. Here, the authors show that differences in mortality, rather than thermodynamics, cell size or biomass yield, explain the discrepancy, without the need to invoke yet undiscovered, abundant nitrite oxidizers.
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37
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Lu Y, Xia X, Cheung S, Jing H, Liu H. Differential Distribution and Determinants of Ammonia Oxidizing Archaea Sublineages in the Oxygen Minimum Zone off Costa Rica. Microorganisms 2019; 7:E453. [PMID: 31618850 PMCID: PMC6843251 DOI: 10.3390/microorganisms7100453] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 10/08/2019] [Accepted: 10/13/2019] [Indexed: 11/17/2022] Open
Abstract
Ammonia oxidizing archaea (AOA) are microbes that are widely distributed in the ocean that convert ammonia to nitrite for energy acquisition in the presence of oxygen. Recent study has unraveled highly diverse sublineages within the previously defined AOA ecotypes (i.e., water column A (WCA) and water column B (WCB)), although the eco-physiology and environmental determinants of WCB subclades remain largely unclear. In this study, we examined the AOA communities along the water columns (40-3000 m depth) in the Costa Rica Dome (CRD) upwelling region in the eastern tropical North Pacific Ocean. Highly diverse AOA communities that were significantly different from those in oxygenated water layers were observed in the core layer of the oxygen minimum zone (OMZ), where the dissolved oxygen (DO) concentration was < 2μM. Moreover, a number of AOA phylotypes were found to be enriched in the OMZ core. Most of them were negatively correlated with DO and were also detected in other OMZs in the Arabian Sea and Gulf of California, which suggests low oxygen adaptation. This study provided the first insight into the differential niche partitioning and environmental determinants of various subclades within the ecotype WCB. Our results indicated that the ecotype WCB did indeed consist of various sublineages with different eco-physiologies, which should be further explored.
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Affiliation(s)
- Yanhong Lu
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen 518061, China.
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510220, China.
| | - Shunyan Cheung
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
- Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.
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38
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Muck S, De Corte D, Clifford EL, Bayer B, Herndl GJ, Sintes E. Niche Differentiation of Aerobic and Anaerobic Ammonia Oxidizers in a High Latitude Deep Oxygen Minimum Zone. Front Microbiol 2019; 10:2141. [PMID: 31572345 PMCID: PMC6753893 DOI: 10.3389/fmicb.2019.02141] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 08/30/2019] [Indexed: 12/30/2022] Open
Abstract
To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70-100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 ± 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 ± 5.1%) and bathypelagic waters (85.5 ± 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 ± 6.9 bacterial nirK gene mL-1) and anaerobic ammonia oxidizers (78 ± 322 anammox 16S rRNA genes L-1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a reservoir of genetic and metabolic potential ready to colonize the environment under the predicted increase of OMZs in the ocean. Taken together, our results reinforce the niche partitioning of archaeal ammonia oxidizers based on their distinct metabolic characteristics resulting in the dominance of LAC-AOA in a high latitude deep OMZ. Considering the different ecological roles and functions of the two archaeal ecotypes, the expansion of the zones dominated by the LAC-ecotype might have implications for the nitrogen cycle in the future ocean.
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Affiliation(s)
- Simone Muck
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Daniele De Corte
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Elisabeth L. Clifford
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Barbara Bayer
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J. Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Vienna, Austria
- Ecosystem Oceanography Group (GRECO), Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Palma, Spain
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Reji L, Tolar BB, Smith JM, Chavez FP, Francis CA. Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay. Environ Microbiol 2019; 21:4032-4045. [PMID: 31330081 DOI: 10.1111/1462-2920.14753] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/16/2019] [Accepted: 07/16/2019] [Indexed: 11/29/2022]
Abstract
Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are key players in nutrient cycling, yet large gaps remain in our understanding of their ecology and metabolism. Despite multiple lines of evidence pointing to a central role for copper-containing nitrite reductase (NirK) in AOA metabolism, the thaumarchaeal nirK gene is rarely studied in the environment. In this study, we examine the diversity of nirK in the marine pelagic environment, in light of previously described ecological patterns of pelagic thaumarchaeal populations. Phylogenetic analyses show that nirK better resolves diversification patterns of marine Thaumarchaeota, compared to the conventionally used marker gene amoA. Specifically, we demonstrate that the three major phylogenetic clusters of marine nirK correspond to the three 'ecotype' populations of pelagic Thaumarchaeota. In this context, we further examine the relative distributions of the three variant groups in metagenomes and metatranscriptomes representing two depth profiles in coastal Monterey Bay. Our results reveal that nirK effectively tracks the dynamics of thaumarchaeal ecotype populations, particularly finer-scale diversification patterns within major lineages. We also find evidence for multiple copies of nirK per genome in a fraction of thaumarchaeal cells in the water column, which must be taken into account when using it as a molecular marker.
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Affiliation(s)
- Linta Reji
- Department of Earth System Science, Stanford University, Stanford, CA
| | - Bradley B Tolar
- Department of Earth System Science, Stanford University, Stanford, CA
| | - Jason M Smith
- Monterey Bay Aquarium Research Institute, Moss Landing, CA.,Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA
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Bayer B, Hansman RL, Bittner MJ, Noriega-Ortega BE, Niggemann J, Dittmar T, Herndl GJ. Ammonia-oxidizing archaea release a suite of organic compounds potentially fueling prokaryotic heterotrophy in the ocean. Environ Microbiol 2019; 21:4062-4075. [PMID: 31336026 PMCID: PMC6899801 DOI: 10.1111/1462-2920.14755] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 01/25/2023]
Abstract
Ammonia‐oxidizing archaea (AOA) constitute a considerable fraction of microbial biomass in the global ocean, comprising 20%–40% of the ocean's prokaryotic plankton. However, it remains enigmatic to what extent these chemolithoautotrophic archaea release dissolved organic carbon (DOC). A combination of targeted and untargeted metabolomics was used to characterize the exometabolomes of three model AOA strains of the Nitrosopumilus genus. Our results indicate that marine AOA exude a suite of organic compounds with potentially varying reactivities, dominated by nitrogen‐containing compounds. A significant fraction of the released dissolved organic matter (DOM) consists of labile compounds, which typically limit prokaryotic heterotrophic activity in open ocean waters, including amino acids, thymidine and B vitamins. Amino acid release rates corresponded with ammonia oxidation activity and the three Nitrosopumilus strains predominantly released hydrophobic amino acids, potentially as a result of passive diffusion. Despite the low contribution of DOC released by AOA (~0.08%–1.05%) to the heterotrophic prokaryotic carbon demand, the release of physiologically relevant metabolites could be crucial for microbes that are auxotrophic for some of these compounds, including members of the globally abundant and ubiquitous SAR11 clade.
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Affiliation(s)
- Barbara Bayer
- Division of Bio-Oceanography, Department of Limnology and Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Vienna, 1090, Austria
| | - Roberta L Hansman
- Division of Bio-Oceanography, Department of Limnology and Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Vienna, 1090, Austria.,International Atomic Energy Agency - Environment Laboratories, Radioecology Laboratory, 98000, Monaco, Monaco
| | - Meriel J Bittner
- Division of Bio-Oceanography, Department of Limnology and Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Vienna, 1090, Austria
| | - Beatriz E Noriega-Ortega
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, 26129, Oldenburg, Germany
| | - Jutta Niggemann
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, 26129, Oldenburg, Germany
| | - Thorsten Dittmar
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, 26129, Oldenburg, Germany
| | - Gerhard J Herndl
- Division of Bio-Oceanography, Department of Limnology and Bio-Oceanography, Centre of Functional Ecology, University of Vienna, Vienna, 1090, Austria.,Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, 1790, AB Den Burg, Texel, The Netherlands
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