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Allometric scaling of interspecific RNA transcript abundance to extend the use of metatranscriptomics in characterizing complex communities

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Molecular ecology resources 2023年第1期23卷 52-63页

作者： Mark Louie D Lopez Ya-Ying Lin Stephan Q Schneider Chih-Hao Hsieh Fuh-Kwo Shiah Ryuji J Machida Biodiversity Program Taiwan International Graduate Program Academia Sinica and National Taiwan Normal University Taipei Taiwan. Department of Life Science National Taiwan Normal University Taipei Taiwan. Department of Biochemistry and Microbiology University of Victoria Victoria Canada. Biodiversity Research Center Academia Sinica Taipei Taiwan. Institute of Organismic and Cellular Biology Academia Sinica Taipei Taiwan. Institute of Oceanography National Taiwan University Taipei Taiwan. Environmental Change Research Center Academia Sinica Taipei Taiwan.

Metatranscriptomics allows profiling of community mRNA and rRNA transcript abundance under certain environmental conditions. However, variations in the proportion of RNA transcripts across different community size structures remain less explained, thus limiting the possible applications of metatranscriptomics in community studies. Here, we extended the assumptions of the growth-rate hypothesis (GRH) and the metabolic theory of ecology (MTE) to validate the allometric scaling of interspecific RNA transcript (mRNA and rRNA) abundance through metatranscriptomic analysis of mock communities consisting of model organisms. The results suggest that body size imposes significant constraints on RNA transcript abundance. Interestingly, the relationship between the total mitochondrial transcript abundance (mRNA and rRNA slopes were -0.30 and -0.28, respectively) and body size aligned with the MTE assumptions with slopes close to -¼, while the nuclear transcripts displayed much steeper slopes (mRNA and rRNA slopes were -0.33 and -0.40, respectively). The assumed temperature dependence was not observed in this study. At the gene level, the allometric slopes range from 0 to -1. Overall, the above results showed that larger individuals have lesser RNA transcript abundance per tissue mass than smaller ones regardless of temperature. Analyses of field-collected microcrustacean zooplankton samples demonstrated that the correction of size effect, using the allometric exponents derived from the model organism mock community, explains better the patterns of interspecific RNA transcripts abundance within the metatranscriptome. Integrating allometry with metatranscriptomics can extend the use of RNA transcript reads in estimating ecological processes within complex communities.

关键词： body size scaling growth-rate hypothesis metabolic theory of ecology metatranscriptomics

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Microbiome heterogeneity in tissues of the coral, Fimbriaphyllia (Euphyllia) ancora

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Environmental Microbiology Reports 2024年第4期16卷 e13310页

作者： Chuang, Po-Shun Wang, Tzu-Haw Lu, Chih-Ying Tandon, Kshitij Shikina, Shinya Tang, Sen-Lin Biodiversity Research Center Academia Sinica Institute of Oceanography National Taiwan University Molecular and Biological Agricultural Sciences Program Taiwan International Graduate Program National Chung Hsing University and Academia Sinica Graduate Institute of Biotechnology National Chung Hsing University School of BioSciences The University of Melbourne Institute of Marine Environment and Ecology National Taiwan Ocean University Center of Excellence for the Oceans National Taiwan Ocean University Taiwan Ocean Genome Center National Taiwan Ocean University

Coral microbiomes differ in the mucus, soft tissue and skeleton of a coral colony, but whether variations exist in different tissues of a single polyp is unknown. In the stony coral, Fimbriaphyllia ancora, we identified 8,994 amplicon sequencing variants (ASVs) in functionally differentiated polyp tissues, i.e., tentacles, body wall, mouth and pharynx, mesenterial filaments, and gonads (testes and ovaries), with a large proportion of ASVs specific to individual tissues. However, shared ASVs comprised the majority of microbiomes from all tissues in terms of relative abundance. No tissue-specific ASVs were found, except in testes, for which there were only two samples. At the generic level, Endozoicomonas was significantly less abundant in the body wall, where calicoblastic cells reside. On the other hand, several bacterial taxa presented significantly higher abundances in the mouth. Interestingly, although without statistical confirmation, gonadal tissues showed lower ASV richness and relatively high abundances of Endozoicomonas (in ovaries) and Pseudomonas (in testes). These findings provide evidence for microbiome heterogeneity between tissues within coral polyps, suggesting a promising field for future studies of functional interactions between corals and their bacterial symbionts. © 2024 The Author(s). Environmental Microbiology Reports published by John Wiley & Sons Ltd.

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Evidences showing wide presence of small genomic aberrations in chronic lymphocytic leukemia

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BMC Research Notes 2010年第1期3卷 1-12页

作者： Kim, Yeong C. Jung, Yong-Chul Chen, Jun Alhasan, Ali H. Kaewsaard, Parawee Zhang, Yanming Ma, Shuo Rosen, Steve Wang, San Ming Department of Genetics Cell Biology and Anatomy College of Medicine University of Nebraska Medical Center Nebraska United States Northshore University Healthsystem Research Institute Evanston IL 60201 United States McCormick School of Engineering and Applied Science Northwestern University IL United States Department of Medicine University of Chicago Pritzker School of Medicine IL United States Robert H. Lurie Comprehensive Cancer Center Northwestern University IL United States ACGT Inc. IL United States School of Oceanography and Environment Xiamen University Xiamen China Interdepartmental Biological Science Graduate Program Northwestern University IL United States Food and Drug Administration Bangkok Thailand

Background. Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in the western population. Although genetic factors are considered to contribute to CLL etiology, at present genomic aberrations identified in CLL are limited compared with those identified in other types of leukemia, which raises the question of the degree of genetic influence on CLL. We performed a high-resolution genome scanning study to address this issue. Findings. Using the restriction paired-end-based Ditag Genome Scanning technique, we analyzed three primary CLL samples at a kilobase resolution, and further validated the results in eight primary CLL samples including the two used for ditag collection. From 51,632 paired-end tags commonly detected in the three CLL samples representing 5% of the HindIII restriction fragments in the genomes, we identified 230 paired-end tags that were present in all three CLL genomes but not in multiple normal human genome reference sequences. Mapping the full-length sequences of the fragments detected by these unmapped tags in seven additional CLL samples confirmed that these are the genomic aberrations caused by small insertions and deletions, and base changes spreading across coding and non-coding regions. Conclusions. Our study identified hundreds of loci with insertion, deletion, base change, and restriction site polymorphism present in both coding and non-coding regions in CLL genomes, indicating the wide presence of small genomic aberrations in chronic lymphocytic leukemia. Our study supports the use of a whole genome sequencing approach for comprehensively decoding the CLL genome for better understanding of the genetic defects in CLL. © 2010 Wang et al;licensee BioMed Central Ltd.

关键词： Chronic Lymphocytic Leukemia Genomic Aberration HindIII Restriction Site Chronic Lymphocytic Leukemia Sample Human Genome Reference Sequence

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Coherence of transport variability along outer Banda Arcs

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IOP Conference Series: Earth and Environmental Science 2018年第1期176卷

作者： V C Masoleh A S Atmadipoera Graduate Program in Marine Sciences Bogor Agricultural University (IPB Physical Oceanography Laboratory Dept. of Marine Science and Technology-IPB

Previous study hypothesized that the Pacific equatorial waves could enter into the interior Indonesian Seas and influenced the Indonesian Throughflow (ITF) along its eastern pathway. Here we investigate the variability of volume transport in the upper 500 m depth and its coherency along the outer Banda Arcs (OBA) channel from Ceram Sea (CS) to Aru Basin (AB) to western Timor Passage (TP) using daily INDESO model output (2008-2014). As expected, mean volume transport along OBA is in clock-wise direction: +1.04 (±1.54) Sv eastward in CS, -0.61 (±0.79) Sv southward in AB, and -8.42 (±2.05) Sv westward in TP, respectively. The vertical structure of currents is prominently intensified in the upper 300 m layer. Scales of transport variability in CS and AB are dominated by annual period with secondary in intraseasonal (ISV) period. In contrast, TP dominant periodicities are on the semiannual and ISV scales. Transport variability on ISV 30-43 days period among CS - AB - TP shows a significant coherence (>0.8) and phase difference (2-5 days) with signal in CS leading to AB and TP. This suggests a presence of Pacific equatorial waves which propagate along OBA channel.

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Field chemistry

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Science (New York, N.Y.) 1992年第5041期255卷 218-9页

作者： J M Edmond H N Edmonds Department of Earth Atmospheric and Planetary Sciences and MIT/WHOI Joint Graduate Program in Oceanography Massachusetts Institute of Technology Cambridge MA 02139

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LOOKING TO THE FUTURE

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Limnology and oceanography Bulletin 2021年第1期30卷 18-19页

作者： Hunter Hughes Maha J. Cziesielski Connor Love Catherine Nowakowski Angelique Rosa Marín Keiko W. Wilkins Department of Geological Sciences University of North Carolina at Chapel Hill Chapel Hill NC USA Trinomics Rotterdam The Netherlands Interdepartmental Graduate Program for Marine Sciences University of California Santa Barbara CA USA Department of Oceanography University of Rhode Island Narragansett RI USA School of the Environment Florida Agricultural and Mechanical University Tallahassee FL USA Kewalo Marine Laboratory University of Hawaii at Manoa Honolulu HI USA

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Nitrogen subsidies to pelagic food webs through profundal methane-oxidising bacteria in oligotrophic fresh water

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Freshwater Biology 2024年第5期69卷 679-691页

作者： dela Paz, Erica Silk P. Okuda, Noboru Ho, Pei-Chi Lin, Fan-Sian Hsieh, Chih-hao Lai, Chao-Chen Fujibayash, Megumu Shiah, Fuh-Kwo Ko, Chia-Ying Institute of Fisheries Science National Taiwan University Taipei Taiwan Microalgal Systematics and Phycology Research Unit Center for Natural Science and Environmental Research De La Salle University Manila Philippines Department of Biology College of Science De La Salle University Manila Philippines Research Center for Humanity and Nature Kyoto Japan Research Center for Inland Seas Graduate School of Science Kobe University Kobe Japan Institute of Oceanography National Taiwan University Taipei Taiwan Research Center for Environmental Changes Academia Sinica Taipei Taiwan Instituted of Ecology and Evolutionary Biology & Master's Program in Biodiversity National Taiwan University Taipei Taiwan Department of Science Education National Taipei University of Education Taipei Taiwan Faculty of Engineering Kyushu University Fukuoka City Japan

Nutrient subsidy of methane-oxidising bacteria (MOB), an alternative basal resource, to plankton communities through pelagic-benthic coupling is expected to alter carbon-to-nitrogen (C/N) ratios and biomass of zooplankton, and affect biological processes in aquatic food webs. Previous studies indicate that most MOB nutrient subsidies to zooplankton are focused largely on C subsidies;nevertheless, considering that N is important to zooplankton and phytoplankton growth, a better understanding of MOB N subsidies to plankton communities is needed. We examined changes in nutrients, phytoplankton mass-specific productivity, MOB reliance, C/N ratios and biomass of zooplankton between summer stratification and winter mixing periods based on in situ investigation in a subtropical deep oligotrophic freshwater ecosystem during 2010–2014. The results revealed that with increasing reliance on MOB during the winter mixing period, zooplankton C/N ratios decreased and had a significantly nonlinearly inverse relationship with zooplankton biomass. The negative relationship between zooplankton biomass and phytoplankton mass-specific productivity was further observed in synchronous time. The profundal MOB enhanced pelagic-profundal coupling and served as an alternative N support for pelagic plankton food webs during the winter and/or less productive seasons, adding to greater understanding of the role of methanotrophs in aquatic food webs. © 2024 John Wiley & Sons Ltd.

关键词： freshwater methane-oxidising bacteria nutrient subsidy phytoplankton zooplankton

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Science Advances 2023年第47期9卷

作者： Chiou, Yu-Jing Chan, Ya-Fan Yu, Sheng-Ping Lu, Chih-Ying Hsiao, Silver Sung-Yun Chiang, Pei-Wen Hsu, Ting-Chang Liu, Po-Yu Wada, Naohisa Lee, Yu Jane, Wann-Neng Lee, Der-Chuen Huang, Yu-Wen Tang, Sen-Lin Institute of Oceanography National Taiwan University Taipei106 Taiwan Biodiversity Research Center Academia Sinica Taipei115 Taiwan Department of Microbiology Soochow University Taipei111 Taiwan Molecular and Biological Agricultural Sciences Program Taiwan International Graduate Program National Chung Hsing University Academia Sinica Taipei115 Taiwan Graduate Institute of Biotechnology National Chung Hsing University Taichung402 Taiwan Institute of Astronomy and Astrophysics Academia Sinica Taipei115 Taiwan School of Medicine College of Medicine National Sun Yat-Sen University Kaohsiung804 Taiwan Department of Chemistry National Tsing Hua University Hsinchu300 Taiwan Institute of Plant and Microbial Biology Academia Sinica Taipei115 Taiwan

Endozoicomonas are often predominant bacteria and prominently important in coral health. Their role in dimethylsulfoniopropionate (DMSP) degradation has been a subject of discussion for over a decade. A previous study found that Endozoicomonas degraded DMSP through the dddD pathway. This process releases dimethyl sulfide, which is vital for corals coping with thermal stress. However, little is known about the related gene regulation and metabolic abilities of DMSP metabolism in Endozoicomonadaceae. In this study, we isolated a novel Endozoicomonas DMSP degrader and observed a distinct DMSP metabolic trend in two phylogenetically close dddDharboring Endozoicomonas species, confirmed genetically by comparative transcriptomic profiling and visualization of the change of DMSP stable isotopes in bacterial cells using nanoscale secondary ion spectrometry. Furthermore, we found that DMSP cleavage enzymes are ubiquitous in coral Endozoicomonas with a preference for having DddD lyase. We speculate that harboring DMSP degrading genes enables Endozoicomonas to successfully colonize various coral species across the globe. Copyright © 2023 The Authors,

关键词： Metabolism

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Communicating Hope for Coral Reefs

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Limnology and oceanography Bulletin 2021年第1期30卷 15-16页

作者： Catherine Nowakowski Hunter Hughes Connor Love Angelique Rosa Marin Keiko Wilkins Maha J. Cziesielski Department of Oceanography University of Rhode Island Narragansett RI USA Department of Geological Sciences University of North Carolina at Chapel Hill Chapel Hill NC USA Interdepartmental Graduate Program for Marine Sciences University of California Santa Barbara Santa Barbara CA USA School of the Environment Florida Agricultural and Mechanical University Tallahassee FL USA Kewalo Marine Laboratory University of Hawai'i at Mānoa Honolulu HI USA Trinomics Rotterdam The Netherlands

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Global Warming and the Power-Laws of Ecology

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Atmospheric and Climate Sciences 2012年第1期2卷 8-13页

作者： Joao D.T.Arruda-Neto Maria C.Bittencourt-Oliveira Alrenice C.Castro Tulio E.Rodrigues Joseph Harari Joel Mesa Godofredo C.Genofre Physics Institute University of Sao PauloSao PauloBrazil CEPESq/UniItalo Italy-Brazilian University CenterSao PauloBrazil Laboratory of Cyanobacteria ESALQUniversity of Sao PauloPiracicabaBrazil PROCAM Interdisciplinary Graduate Program on Environmental SciencesUniversity of Sao PauloSao PauloBrazil Institute of Oceanography University of Sao PauloSao PauloBrazil Institute of Biosciences Sao Paulo State UniversityBotucatuBrazil Institute of Biosciences University of Sao PauloSao PauloBrazil

A model based on Watson’s power law for the species-area relationship predicts that full global warming, projected up to the year 2050, could provoke the disappearance of roughly one-quarter of existing species. Here, an alternative approach is worked out, based on the combination of two ecology laws: Taylor and Watson’s power laws, where the former relates species variability with their mean abundance. Just how severely global warming would affect not only the number but the diversity of the surviving species is addressed by this approach, while at the same time giving indications for the post-disaster fate of the remaining species (extinction or recovery).

关键词： Global Warming Species Extinction Ecology Power-Laws Species Variability Model

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