1
|
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.
Collapse
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
| |
Collapse
|
2
|
Xu Y, Lu J, Huang S, Zhao J. Submerged plants alleviated the impacts of increased ammonium pollution on anammox bacteria and nirS denitrifiers in the rhizosphere. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:58755-58767. [PMID: 34120278 DOI: 10.1007/s11356-021-14715-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
Excess nitrogen input into water bodies can cause eutrophication and affect the community structure and abundance of the nitrogen-transforming microorganisms; thus, it is essential to remove nitrogen from eutrophic water bodies. Aquatic plants can facilitate the growth of rhizosphere microorganisms. This study investigated the impact of ammonium pollution on the anammox and denitrifying bacteria in the rhizosphere of a cultivated submerged macrophyte, Potamogeton crispus (P. crispus) by adding three different concentrations of slow-release urea (0, 400, 600 mg per kg sediment) to the sediment to simulate different levels of nitrogen pollution in the lake. Results showed that the ammonium concentrations in the interstitial water under three pollution treatments were significantly different, but the nitrate concentration remained stable. The abundance of anammox 16S rRNA and nitrite reductase (nirS) gene in rhizosphere sediments exhibited no significant differences under the three pollution conditions. The increase in the nitrogen pollution levels did not significantly affect the growth of anammox bacteria and nirS denitrifying bacteria (denitrifiers). The change trend of the abundance ratio of (anammox 16S rRNA)/nirS in different nitrogen treatment groups on the same sampling date was very close, indicating that this ratio was not affected by ammonium pollution levels when P. crispus existed. The redundancy analysis showed that there was a positive correlation between the abundance of anammox 16S rRNA and nirS gene and that the abundance of these bacteria was significantly affected by the mole ratio of NH4+/NO3-. This study reveals that submerged plants weaken the environmental changes caused by ammonia pollution in the rhizosphere, thereby avoiding strong fluctuation of anammox bacteria and nirS denitrifiers.
Collapse
Affiliation(s)
- Yangfan Xu
- Research and Development Center of Transport Industry of Intelligent Manufacturing Technologies of Transport Infrastructure, Wuhan, 430040, China
- Key Laboratory of Large-span Bridge Construction Technology, Wuhan, 430040, China
- CCCC Second Harbor Engineering Company Ltd., Wuhan, 430040, China
| | - Jing Lu
- Australian Rivers Institute, Griffith University, QLD, Nathan, 4111, Australia
| | - Shanshan Huang
- Laboratory of Eco-Environmental Engineering Research, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Jianwei Zhao
- Laboratory of Eco-Environmental Engineering Research, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China.
| |
Collapse
|
3
|
Xiao Y, Yin X, Chen L, Wang J, Wang Y, Liu G, Hua Y, Wan X, Xiao N, Zhao J, Zhu D. Effects of illumination on nirS denitrifying and anammox bacteria in the rhizosphere of submerged macrophytes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 760:143420. [PMID: 33189380 DOI: 10.1016/j.scitotenv.2020.143420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/08/2020] [Accepted: 10/26/2020] [Indexed: 06/11/2023]
Abstract
Visibility in lakes can decrease due to increases in the amounts of suspended solids and algae, which inhibits the growth of submerged macrophytes. However, the understanding about whether illumination reduction affects the nitrogen-cycling microorganisms in the rhizosphere of submerged macrophytes, is limited. The abundance and biodiversity of nirS denitrifying and anammox bacteria in the rhizosphere of Potamogeton crispus were studied under 0% (natural light), 20%, 40%, and 60% shading treatments. The abundance of the nirS gene was highest under 60% shading treatment, while the anammox 16S rRNA gene was highest under 40% shading treatment. Moreover, the abundance of the two genes were lower under natural light than under shading conditions during most sampling periods. The quantitative ratio of the two gene (anammox 16S rRNA to nirS gene) abundance fluctuated wildly with the distance away from the roots, under natural light and 20% shading treatment. However, the ratio varied relatively little under 40% and 60% shading treatments. The diversity of nirS denitrifying bacteria was high in the rhizosphere, while the diversity of anammox bacteria was low, and Candidatus Brocadia fulgida was dominant. This study revealed that illumination reduction not only facilitated the growth of nirS denitrifying and anammox bacteria in the rhizosphere, but also weakened the competition between the two bacteria.
Collapse
Affiliation(s)
- Yang Xiao
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingjia Yin
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Lijuan Chen
- Key Laboratory of Ecohydrology of Inland River Basin, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Jing Wang
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuchun Wang
- Department of Water Environment, China Institute of Water Resources and Hydropower Research, Beijing 100038, China; State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Institute of Water Resources and China Hydropower Research, Beijing 100038, China.
| | - Guanglong Liu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yumei Hua
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoqiong Wan
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Naidong Xiao
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianwei Zhao
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Duanwei Zhu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
4
|
Wang F, Lin D, Li W, Dou P, Han L, Huang M, Qian S, Yao J. Meiofauna promotes litter decomposition in stream ecosystems depending on leaf species. Ecol Evol 2020; 10:9257-9270. [PMID: 32953059 PMCID: PMC7487239 DOI: 10.1002/ece3.6610] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 11/10/2022] Open
Abstract
Litter decomposition, a fundamental process of nutrient cycling and energy flow in freshwater ecosystems, is driven by a diverse array of decomposers. As an important component of the heterotrophic food web, meiofauna can provide a trophic link between leaf-associated microbes (i.e., bacteria and fungi)/plant detritus and macroinvertebrates, though their contribution to litter decomposition is not well understood. To investigate the role of different decomposer communities in litter decomposition, especially meiofauna, we compared the litter decomposition of three leaf species with different lignin to nitrogen ratios in litter bags with different mesh sizes (0.05, 0.25, and 2 mm) in a forested stream, in China for 78 days. The meiofauna significantly enhanced the decomposition of leaves of high-and medium- quality, while decreasing (negative effect) or increasing (positive effect) the fungal biomass and diversity. Macrofauna and meiofauna together contributed to the decomposition of low-quality leaf species. The presence of meiofauna and macrofauna triggered different aspects of the microbial community, with their effects on litter decomposition varying as a function of leaf quality. This study reveals that the meiofauna increased the trophic complexity and modulated their interactions with microbes, highlighting the important yet underestimated role of meiofauna in detritus-based ecosystems.
Collapse
Affiliation(s)
- Fang Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco‐EnvironmentMinistry of EducationChongqing UniversityChongqingChina
- College of Environment and EcologyChongqing UniversityChongqingChina
| | - Dunmei Lin
- Key Laboratory of the Three Gorges Reservoir Region's Eco‐EnvironmentMinistry of EducationChongqing UniversityChongqingChina
- College of Environment and EcologyChongqing UniversityChongqingChina
| | - Wei Li
- Key Laboratory of the Three Gorges Reservoir Region's Eco‐EnvironmentMinistry of EducationChongqing UniversityChongqingChina
- College of Environment and EcologyChongqing UniversityChongqingChina
| | - Pengpeng Dou
- Key Laboratory of the Three Gorges Reservoir Region's Eco‐EnvironmentMinistry of EducationChongqing UniversityChongqingChina
- College of Environment and EcologyChongqing UniversityChongqingChina
| | - Le Han
- Key Laboratory of the Three Gorges Reservoir Region's Eco‐EnvironmentMinistry of EducationChongqing UniversityChongqingChina
- College of Environment and EcologyChongqing UniversityChongqingChina
| | - Mingfen Huang
- Key Laboratory of the Three Gorges Reservoir Region's Eco‐EnvironmentMinistry of EducationChongqing UniversityChongqingChina
- College of Environment and EcologyChongqing UniversityChongqingChina
| | - Shenhua Qian
- Key Laboratory of the Three Gorges Reservoir Region's Eco‐EnvironmentMinistry of EducationChongqing UniversityChongqingChina
- College of Environment and EcologyChongqing UniversityChongqingChina
| | - Jingmei Yao
- Key Laboratory of the Three Gorges Reservoir Region's Eco‐EnvironmentMinistry of EducationChongqing UniversityChongqingChina
- College of Environment and EcologyChongqing UniversityChongqingChina
| |
Collapse
|
5
|
Denitrification characterization of dissolved oxygen microprofiles in lake surface sediment through analyzing abundance, expression, community composition and enzymatic activities of denitrifier functional genes. AMB Express 2019; 9:129. [PMID: 31428884 PMCID: PMC6702497 DOI: 10.1186/s13568-019-0855-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/08/2019] [Indexed: 12/12/2022] Open
Abstract
The responses of denitrifiers and denitrification ability to dissolved oxygen (DO) concent in different layers of surface lake sediments are still poorly understood. Here, the optimal denitrification condition was constructed based on response surface methodology (RSM) to analyze the denitrification characteristics of surface sediments. The aerobic zone (AEZ), hypoxic zone (HYZ), up-anoxic zone (ANZ-1) and sub-anoxic zone (ANZ-2) were partitioned based on the oxygen contents, and sediments were collected using a customized-designed sub-millimeter scale sampling device. Integrated real-time quantitative PCR, Illumina Miseq-based sequencing and denitrifying enzyme activities analysis revealed that denitrification characteristics varied among different DO layers. Among the four layers, the DNA abundance and RNA expression levels of norB, nirS and nosZ were the highest at the aerobic layer, hypoxic layer and up-axoic layer, respectively. The hypoxia and up-anaerobic layer were the active nitrogen removal layers, since these two layers displayed the highest DNA abundance, RNA expression level and enzyme activities of denitrification functional genes. The abundance of major denitrifying bacteria showed significant differences among layers, with Azoarcus, Pseudogulbenkiania and Rhizobium identified as the main nirS, nirK and nosZ-based denitrifiers. Pearson’s correlation revealed that the response of denitrifiers to environmental factors differed greatly among DO layers. Furthermore, napA showed higher DNA abundance and RNA expression level in the aerobic and hypoxic layers than anaerobic layers, indicating that aerobic denitrifiers might play important roles at these layers.
Collapse
|