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Piertney SB, Wenzel M, Jamieson AJ. Large effective population size masks population genetic structure in Hirondellea amphipods within the deepest marine ecosystem, the Mariana Trench. Mol Ecol 2023; 32:2206-2218. [PMID: 36808786 DOI: 10.1111/mec.16887] [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: 08/26/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/20/2023]
Abstract
The examination of genetic structure in the deep-ocean hadal zone has focused on divergence between tectonic trenches to understand how environment and geography may drive species divergence and promote endemism. There has been little attempt to examine localized genetic structure within trenches, partly because of logistical challenges associated with sampling at an appropriate scale, and the large effective population sizes of species that can be sampled adequately may mask underlying genetic structure. Here we examine genetic structure in the superabundant amphipod Hirondellea gigas in the Mariana Trench at depths of 8126-10,545 m. RAD sequencing was used to identify 3182 loci containing 43,408 single nucleotide polymorphisms (SNPs) across individuals after stringent pruning of loci to prevent paralogous multicopy genomic regions being erroneously merged. Principal components analysis of SNP genotypes resolved no genetic structure between sampling locations, consistent with a signature of panmixia. However, discriminant analysis of principal components identified divergence between all sites driven by 301 outlier SNPs in 169 loci and significantly associated with latitude and depth. Functional annotation of loci identified differences between singleton loci used in analysis and paralogous loci pruned from the data set and also between outlier and nonoutlier loci, all consistent with hypotheses explaining the role of transposable elements driving genome dynamics. This study challenges the traditional perspective that highly abundant amphipods within a trench form a single panmictic population. We discuss the findings in relation to eco-evolutionary and ontogenetic processes operating in the deep sea, and highlight key challenges associated with population genetic analysis in nonmodel systems with inherent large effective population sizes and genomes.
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Affiliation(s)
| | - Marius Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Alan J Jamieson
- Minderoo-UWA Deep-Sea Research Centre, School of Biological Sciences and Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia
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Okada S, Chen C, Watanabe HK, Isobe N, Takai K. Unusual bromine enrichment in the gastric mill and setae of the hadal amphipod Hirondellea gigas. PLoS One 2022; 17:e0272032. [PMID: 35925928 PMCID: PMC9352070 DOI: 10.1371/journal.pone.0272032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 07/12/2022] [Indexed: 11/18/2022] Open
Abstract
The hadal amphipod Hirondellea gigas is an emblematic animal of the Pacific trenches, and has a number of special adaptations to thrive in this ‘extreme’ environment, which includes the deepest part of the Earth’s ocean. One such adaptation that has been suggested is the presence of an ‘aluminum gel shield’ on the surface of its body in order to prevent the dissolution of calcitic exoskeleton below the carbonate compensation depth. However, this has not been investigated under experimental conditions that sufficiently prevent aluminum artefacts, and the possibility of other elements with similar characteristic X-ray energy as aluminum (such as bromine) has not been considered. Here, we show with new electron microscopy data gathered under optimized conditions to minimize aluminum artefacts that H. gigas actually does not have an aluminum shield–instead many parts of its body are enriched in bromine, particularly gastric ossicles and setae. Results from elemental analyses pointed to the use of calcite partially substituted with magnesium by H. gigas in its exoskeleton, in order to suppress dissolution. Our results exemplify the necessity of careful sample preparation and analysis of the signals in energy-dispersive X-ray spectroscopic analysis, and the importance of analyses at different electron energies.
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Affiliation(s)
- Satoshi Okada
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
- * E-mail:
| | - Chong Chen
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Hiromi Kayama Watanabe
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Noriyuki Isobe
- Biogeochemistry Research Center, Research Institute for Marine Resources Utilization (MRU), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
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Du M, Peng X, Zhang H, Ye C, Dasgupta S, Li J, Li J, Liu S, Xu H, Chen C, Jing H, Xu H, Liu J, He S, He L, Cai S, Chen S, Ta K. Geology, environment, and life in the deepest part of the world's oceans. ACTA ACUST UNITED AC 2021; 2:100109. [PMID: 34557759 PMCID: PMC8454626 DOI: 10.1016/j.xinn.2021.100109] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023]
Abstract
The hadal zone, mostly comprising of deep trenches and constituting of the deepest part of the world’s oceans, represents the least explored habitat but one of the last frontiers on our planet. The present scientific understanding of the hadal environment is still relatively rudimentary, particularly in comparison with that of shallower marine environments. In the last 30 years, continuous efforts have been launched in deepening our knowledge regarding the ecology of the hadal trench. However, the geological and environmental processes that potentially affect the sedimentary, geochemical and biological processes in hadal trenches have received less attention. Here, we review recent advances in the geology, biology, and environment of hadal trenches and offer a perspective of the hadal science involved therein. For the first time, we release high-definition images taken by a new full-ocean-depth manned submersible Fendouzhe that reveal novel species with an unexpectedly high density, outcrops of mantle and basaltic rocks, and anthropogenic pollutants at the deepest point of the world’s ocean. We advocate that the hydration of the hadal lithosphere is a driving force that influences a variety of sedimentary, geochemical, and biological processes in the hadal trench. Hadal lithosphere might host the Earth’s deepest subsurface microbial ecosystem. Future research, combined with technological advances and international cooperation, should focus on establishing the intrinsic linkage of the geology, biology, and environment of the hadal trenches. This paper provides a comprehensive review on hadal geology, environment, and biology, as well as potential interactions among them For the first time, we release high-definition images taken by a new full-ocean-depth manned submersible Fendouzhe The hydration of the hadal lithosphere is a driving force that influences a variety of sedimentary, geochemical, and biological processes in the hadal trench The development of deep-sea technology and international cooperation will greatly promote the progress of hadal science
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Affiliation(s)
- Mengran Du
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Xiaotong Peng
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- Corresponding author
| | - Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Cong Ye
- China Ship Scientific Research Center, Wuxi 214082, China
| | - Shamik Dasgupta
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Jiwei Li
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Jiangtao Li
- State Key Lab of Marine Geology, Tongji University, Shanghai 200092, China
| | - Shuangquan Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Hengchao Xu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Chuanxu Chen
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Hongmei Jing
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Hongzhou Xu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Jun Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Shunping He
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Lisheng He
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Shanya Cai
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Shun Chen
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Kaiwen Ta
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
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Drozdova P, Kizenko A, Saranchina A, Gurkov A, Firulyova M, Govorukhina E, Timofeyev M. The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae). BMC Ecol Evol 2021; 21:81. [PMID: 33971810 PMCID: PMC8108468 DOI: 10.1186/s12862-021-01806-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/20/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Vision is a crucial sense for the evolutionary success of many animal groups. Here we explore the diversity of visual pigments (opsins) in the transcriptomes of amphipods (Crustacea: Amphipoda) and conclude that it is restricted to middle (MWS) and long wavelength-sensitive (LWS) opsins in the overwhelming majority of examined species. RESULTS We evidenced (i) parallel loss of MWS opsin expression in multiple species (including two independently evolved lineages from the deep and ancient Lake Baikal) and (ii) LWS opsin amplification (up to five transcripts) in both Baikal lineages. The number of LWS opsins negatively correlated with habitat depth in Baikal amphipods. Some LWS opsins in Baikal amphipods contained MWS-like substitutions, suggesting that they might have undergone spectral tuning. CONCLUSIONS This repeating two-step evolutionary scenario suggests common triggers, possibly the lack of light during the periods when Baikal was permanently covered with thick ice and its subsequent melting. Overall, this observation demonstrates the possibility of revealing climate history by following the evolutionary changes in protein families.
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Affiliation(s)
- Polina Drozdova
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
| | | | | | - Anton Gurkov
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
| | - Maria Firulyova
- Computer Technologies Department, ITMO University, St. Petersburg, Russia
| | | | - Maxim Timofeyev
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
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Kobayashi H, Shimoshige H, Nakajima Y, Arai W, Takami H. An aluminum shield enables the amphipod Hirondellea gigas to inhabit deep-sea environments. PLoS One 2019; 14:e0206710. [PMID: 30947320 PMCID: PMC6449124 DOI: 10.1371/journal.pone.0206710] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/17/2019] [Indexed: 11/30/2022] Open
Abstract
The amphipod Hirondellea gigas inhabits the deepest regions of the oceans in extreme high-pressure conditions. However, the mechanisms by which this amphipod adapts to its high-pressure environment remain unknown. In this study, we investigated the elemental content of the exoskeleton of H. gigas specimens captured from the deepest points of the Mariana Trench. The H. gigas exoskeleton contained aluminum, as well as a major amount of calcium carbonate. Unlike other (accumulated) metals, aluminum was distributed on the surface of the exoskeleton. To investigate how H. gigas obtains aluminum, we conducted a metabolome analysis and found that gluconic acid/gluconolactone was capable of extracting metals from the sediment under the habitat conditions of H. gigas. The extracted aluminum ions are transformed into the gel state of aluminum hydroxide in alkaline seawater, and this gel covers the body to protect the amphipod. This aluminum gel is a good material for adaptation to such high-pressure environments.
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Affiliation(s)
- Hideki Kobayashi
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Natsushima, Yokosuka, Japan
- * E-mail:
| | - Hirokazu Shimoshige
- Bio-nano Electronics Research Centre, Toyo University, Kujirai, Kawagoe, Saitama, Japan
| | - Yoshikata Nakajima
- Bio-nano Electronics Research Centre, Toyo University, Kujirai, Kawagoe, Saitama, Japan
| | - Wataru Arai
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Natsushima, Yokosuka, Japan
| | - Hideto Takami
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Natsushima, Yokosuka, Japan
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Wang Y, Zhang H, Yan H, Yin C, Liu Y, Xu Q, Liu X, Zhang Z. Effective Biodegradation of Aflatoxin B1 Using the Bacillus licheniformis (BL010) Strain. Toxins (Basel) 2018; 10:E497. [PMID: 30486278 PMCID: PMC6315853 DOI: 10.3390/toxins10120497] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/16/2018] [Accepted: 11/20/2018] [Indexed: 11/17/2022] Open
Abstract
Aflatoxin B1 (AFB1), a pollutant of agricultural products, has attracted considerable attention in recent years, due to its potential impact on health. In the present study, Bacillus licheniformis (BL010) was demonstrated to efficiently degrade AFB1, reducing over 89.1% of the toxin content within 120 h. A crude enzyme solution of BL010 exhibited the highest degradation level (97.3%) after three induction periods. However, uninduced BL010 bacteria was not capable of reducing AFB1. Furthermore, high performance liquid chromatography (HPLC) analysis showed that while a cell-free extract caused a significant decrease in AFB1 content (93.6%, p < 0.05), cell culture fluid treatment did not significantly degrade AFB1. The biotransformation products of AFB1 were detected and further identified by quadrupole time-of-flight liquid chromatography⁻mass spectrometry (LC-Q-TOF/MS); these corresponded to a molecular formula of C12H14O₄. A sequence analysis of whole BL010 genes with a bioinformatics approach identified the secondary structures of two degrading enzymes (Chia010 and Lac010), providing an important basis for subsequent homology modeling and functional predictions.
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Affiliation(s)
- Ye Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Haiyang Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Hai Yan
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Chunhua Yin
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Yang Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Qianqian Xu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Xiaolu Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| | - Zhongbao Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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Chang WH, Lai AG. Mixed evolutionary origins of endogenous biomass-depolymerizing enzymes in animals. BMC Genomics 2018; 19:483. [PMID: 29925310 PMCID: PMC6011409 DOI: 10.1186/s12864-018-4861-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/11/2018] [Indexed: 11/18/2022] Open
Abstract
Background Animals are thought to achieve lignocellulose digestion via symbiotic associations with gut microbes; this view leads to significant focus on bacteria and fungi for lignocellulolytic systems. The presence of biomass conversion systems hardwired into animal genomes has not yet been unequivocally demonstrated. Results We perform an exhaustive search for glycoside hydrolase (GH) genes from 21 genomes representing major bilaterian (Ecdysozoa, Spiralia, Echinodermata and Chordata) and basal metazoan (Porifera and Cnidaria) lineages. We also assessed the genome of a unicellular relative of Metazoa, Capsaspora owczarzaki and together with comparative analyses on 126 crustacean transcriptomes, we found that animals are living bioreactors at a microscale as they encode enzymatic suites for biomass decomposition. We identified a total of 16,723 GH homologs (2373 genes from animal genomes and 14,350 genes from crustacean transcriptomes) that are further classified into 60 GH families. Strikingly, through phylogenetic analyses, we observed that animal lignocellulosic enzymes have multiple origins, either inherited vertically over millions of years from a common ancestor or acquired more recently from non-animal organisms. Conclusion We have conducted a systematic and comprehensive survey of GH genes across major animal lineages. The ability of biomass decay appears to be determined by animals’ dietary strategies. Detritivores have genes that accomplish broad enzymatic functions while the number of GH families is reduced in animals that have evolved specialized diets. Animal GH candidates identified in this study will not only facilitate future functional genomics research but also provide an analysis platform to identify enzyme candidates with industrial potential. Electronic supplementary material The online version of this article (10.1186/s12864-018-4861-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wai Hoong Chang
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
| | - Alvina G Lai
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
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