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Molik DC, Stahlke AR, Sharma SP, Simmonds TJ, Corpuz RL, Kauwe AN, Schrader JE, Mason CJ, Sim SB, Geib SM. otb: an automated HiC/HiFi pipeline assembles the Prosapia bicincta Genome. G3 (BETHESDA, MD.) 2024; 14:jkae129. [PMID: 38861413 PMCID: PMC11304988 DOI: 10.1093/g3journal/jkae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/04/2024] [Accepted: 06/04/2024] [Indexed: 06/13/2024]
Abstract
The implementation of a new genomic assembly pipeline named only the best (otb) has effectively addressed various challenges associated with data management during the development and storage of genome assemblies. otb, which incorporates a comprehensive pipeline involving a setup layer, quality checks, templating, and the integration of Nextflow and Singularity. The primary objective of otb is to streamline the process of creating a HiFi/HiC genome, aiming to minimize the manual intervention required in the genome assembly process. The 2-lined spittlebug, (Prosapia bicincta, Hemiptera: Cercopidae), a true bug insect herbivore, serves as a practical test case for evaluating otb. The 2-lined spittlebug is both a crucial agricultural pest and a genomically understudied insect belonging to the order Hemiptera. This insect is a significant threat to grasslands and pastures, leading to plant wilting and phytotoxemia when infested. Its presence in tropical and subtropical regions around the world poses a long-term threat to the composition of plant communities in grassland landscapes, impacting rangelands, and posing a substantial risk to cattle production.
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Affiliation(s)
- David C Molik
- Arthropod-Borne Animal Diseases Research Unit, Center for Grain and Animal Health Research, United States Department of Agriculture, Agricultural Research Service, 1515 College Ave, Manhattan, KS 66502, USA
| | - Amanda R Stahlke
- Department of Biological Sciences, Wubben Hall and Science Center, Colorado Mesa University, 1100 North Avenue, Grand Junction, CO 81501-3122, USA
| | - Sharu P Sharma
- Genome Informatics Facility, Iowa State University, 2200 Osborn Drive, Ames, IA 50011-4009, USA
| | - Tyler J Simmonds
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA
| | - Renee L Corpuz
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA
| | - Angela N Kauwe
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA
| | - Jeremy E Schrader
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA
| | - Charles J Mason
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA
| | - Sheina B Sim
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA
| | - Scott M Geib
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA
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Zhang Y, Liu S, Huang XY, Zi HB, Gao T, Ji RJ, Sheng J, Zhi D, Zhang YL, Gong CM, Yang YQ. Altitude as a key environmental factor shaping microbial communities of tea green leafhoppers ( Matsumurasca onukii). Microbiol Spectr 2023; 11:e0100923. [PMID: 37921460 PMCID: PMC10714740 DOI: 10.1128/spectrum.01009-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/19/2023] [Indexed: 11/04/2023] Open
Abstract
IMPORTANCE Host-associated microbial communities play an important role in the fitness of insect hosts. However, the factors shaping microbial communities in wild populations, including environmental factors and interactions among microbial species, remain largely unknown. The tea green leafhopper has a wide geographical distribution and is highly adaptable, providing a suitable model for studying the effect of ecological drivers on microbiomes. This is the first large-scale culture-independent study investigating the microbial communities of M. onukii sampled from different locations. Altitude as a key environmental factor may have shaped microbial communities of M. onukii by affecting the relative abundance of endosymbionts, especially Wolbachia. The results of this study, therefore, offer not only an in-depth view of the microbial diversity of this species but also an insight into the influence of environmental factors.
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Affiliation(s)
- Yong Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
- College of Life Science, Anhui Agricultural University, Hefei, Anhui, China
| | - Song Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Xue-yu Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Hua-bin Zi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Tian Gao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Rui-jie Ji
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Juan Sheng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Dian Zhi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
| | - Ying-lao Zhang
- College of Life Science, Anhui Agricultural University, Hefei, Anhui, China
| | - Chun-mei Gong
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Yun-qiu Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, China
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Li S, Wang J, Tian X, Toufeeq S, Huang W. Immunometabolic regulation during the presence of microorganisms and parasitoids in insects. Front Immunol 2023; 14:905467. [PMID: 37818375 PMCID: PMC10560992 DOI: 10.3389/fimmu.2023.905467] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 09/04/2023] [Indexed: 10/12/2023] Open
Abstract
Multicellular organisms live in environments containing diverse nutrients and a wide variety of microbial communities. On the one hand, the immune response of organisms can protect from the intrusion of exogenous microorganisms. On the other hand, the dynamic coordination of anabolism and catabolism of organisms is a necessary factor for growth and reproduction. Since the production of an immune response is an energy-intensive process, the activation of immune cells is accompanied by metabolic transformations that enable the rapid production of ATP and new biomolecules. In insects, the coordination of immunity and metabolism is the basis for insects to cope with environmental challenges and ensure normal growth, development and reproduction. During the activation of insect immune tissues by pathogenic microorganisms, not only the utilization of organic resources can be enhanced, but also the activated immune cells can usurp the nutrients of non-immune tissues by generating signals. At the same time, insects also have symbiotic bacteria in their body, which can affect insect physiology through immune-metabolic regulation. This paper reviews the research progress of insect immune-metabolism regulation from the perspective of insect tissues, such as fat body, gut and hemocytes. The effects of microorganisms (pathogenic bacteria/non-pathogenic bacteria) and parasitoids on immune-metabolism were elaborated here, which provide guidance to uncover immunometabolism mechanisms in insects and mammals. This work also provides insights to utilize immune-metabolism for the formulation of pest control strategies.
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Affiliation(s)
- Shirong Li
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- College of Life Sciences, Yan’an University, Yan’an, Shaanxi, China
| | - Jing Wang
- College of Life Sciences, Shangrao Normal University, Shangrao, China
| | - Xing Tian
- College of Life Sciences, Yan’an University, Yan’an, Shaanxi, China
| | - Shahzad Toufeeq
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wuren Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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Wu W, Lei JN, Mao Q, Tian YZ, Shan HW, Chen JP. Distribution, Vertical Transmission, and Cooperative Mechanisms of Obligate Symbiotic Bacteria in the Leafhopper Maiestas dorsalis (Hemiptera, Cicadellidea). INSECTS 2023; 14:710. [PMID: 37623420 PMCID: PMC10455556 DOI: 10.3390/insects14080710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/06/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023]
Abstract
Many insects rely on ancient symbiotic bacterial associations for essential nutrition. Auchenorrhyncha commonly harbor two obligate symbionts: Sulcia (Bacteroidetes) and a proteobacterial partner that supplies essential amino acids lacking in their plant-sap diets. In this study focusing on Maiestas dorsalis, we investigated the distribution and vertical transmission of two obligate symbiotic bacteria, Sulcia and Nasuia, within the leafhopper. Sulcia primarily inhabits the external region of the bacteriome, while Nasuia is restricted to the internal region. Both symbionts progressively infiltrate the ovary through the epithelial plug, ultimately reaching the developing primary oocyte. Furthermore, co-phylogenetic analysis suggests a close correlation between the evolution of Auchenorrhyncha insects and the presence of their obligate symbiotic bacteria. Genomic analysis further unveiled the extreme genome reduction of the obligate symbiotic bacteria, with Sulcia retaining genes involved in basic cellular processes and limited energy synthesis, while Nasuia exhibited further gene loss in replication, transcription, translation, and energy synthesis. However, both symbionts retained the genes for synthesizing the essential amino acids required by the host insect. Our study highlights the coevolutionary dynamics between Sulcia, proteobacterial partners, and their insect hosts, shedding light on the intricate nutritional interactions and evolutionary adaptations in Auchenorrhyncha insects.
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Affiliation(s)
- Wei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | | | | | | | | | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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Jin L, Chen X, Pang C, Zhou L, Liu Y, Sun Y, Xu L, Wang Y, Chen Y. Investigation of the antibacterial mechanism of the novel bactericide dioctyldiethylenetriamine (Xinjunan). PEST MANAGEMENT SCIENCE 2023; 79:2780-2791. [PMID: 36924248 DOI: 10.1002/ps.7456] [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: 11/28/2022] [Revised: 03/11/2023] [Accepted: 03/16/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Chemical control is an important method for tackling crop diseases. Clarifying the antibacterial mechanisms of bactericides is useful for developing new bactericides and for continuous plant disease control. In this study, the antibacterial mechanism of a novel bactericide, dioctyldiethylenetriamine (Xinjunan), which affects adenosine triphosphate (ATP) synthesis, was investigated. RESULTS The results of an in vitro inhibition activity assay showed that dioctyldiethylenetriamine inhibited the growth of a variety of plant pathogenic bacteria, especially that of Xanthomonas spp. Scanning electron microscopy demonstrated that dioctyldiethylenetriamine caused cell distortion and rupture. To investigate the molecular mechanism underlying the antibacterial effect of dioctyldiethylenetriamine, transcriptome sequencing (RNA-seq) was performed for Xanthomonas oryzae pv. oryzae (Xoo, PXO99A) treated with dioctyldiethylenetriamine, which has strong antibacterial effects against xanthomonads. The results showed that differentially expressed genes were enriched mainly in the oxidative phosphorylation and tricarboxylic acid (TCA) cycle pathways after treatment. Moreover, the dioctyldiethylenetriamine treatment exhibited reduction in enzyme activities in the TCA cycle, decreased intracellular nicotinamide adenine dinucleotide and ATP contents, and increased accumulation of reactive oxygen species. In addition, dioctyldiethylenetriamine exhibited an inhibitory effect on the growth of other bacterial pathogens by reducing ATP synthesis. CONCLUSION This is the first report of the mechanism by which dioctyldiethylenetriamine inhibits ATP synthesis by affecting oxidative phosphorylation and TCA cycle pathways in bacteria. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Ling Jin
- School of Plant Protection, Anhui Agricultural University, Hefei, China
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Hefei Research Center, Hefei, China
- Key Laboratory of Integrated Crop Pest Management of Anhui Province, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Xing Chen
- School of Plant Protection, Anhui Agricultural University, Hefei, China
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Hefei Research Center, Hefei, China
- Key Laboratory of Integrated Crop Pest Management of Anhui Province, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Chaoyue Pang
- School of Plant Protection, Anhui Agricultural University, Hefei, China
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Hefei Research Center, Hefei, China
- Key Laboratory of Integrated Crop Pest Management of Anhui Province, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Li Zhou
- School of Plant Protection, Anhui Agricultural University, Hefei, China
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Hefei Research Center, Hefei, China
- Key Laboratory of Integrated Crop Pest Management of Anhui Province, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yu Liu
- School of Plant Protection, Anhui Agricultural University, Hefei, China
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Hefei Research Center, Hefei, China
- Key Laboratory of Integrated Crop Pest Management of Anhui Province, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yang Sun
- School of Plant Protection, Anhui Agricultural University, Hefei, China
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Hefei Research Center, Hefei, China
- Key Laboratory of Integrated Crop Pest Management of Anhui Province, School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Liang Xu
- Shandong Vicome Greenland Chemical Co., Ltd, Shandong, China
| | - Yongxing Wang
- Shandong Vicome Greenland Chemical Co., Ltd, Shandong, China
| | - Yu Chen
- School of Plant Protection, Anhui Agricultural University, Hefei, China
- Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, School of Plant Protection, Anhui Agricultural University, Hefei, China
- Anhui Province Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Hefei Research Center, Hefei, China
- Key Laboratory of Integrated Crop Pest Management of Anhui Province, School of Plant Protection, Anhui Agricultural University, Hefei, China
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Deng C, Zhang N, Liang X, Huang T, Li B. Bacillus aryabhattai LAD impacts rhizosphere bacterial community structure and promotes maize plant growth. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:6650-6657. [PMID: 35603593 DOI: 10.1002/jsfa.12032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Plant growth-promoting rhizobacteria may significantly impact the soil microbial community and the growth of plant roots and have critical roles in soil ecosystem functioning. However, the interactions between rhizobacteria and plants are extremely complicated and remain understudied. RESULTS In this study, a Bacillus strain was isolated from a long-term maize colonization soil and identified as Bacillus aryabhattai strain LAD. Laboratory tests showed that B. aryabhattai LAD had phosphate-solubilizing and nitrogen-fixing functions that benefit plant growth. The effects of LAD cultures on the root system development of corn seedlings and the structure of rhizosphere bacterial communities were studied. The most significant stimulations of LAD culture on plant growth were observed at a cell density of 102 CFU mL-1 . Treatment with LAD culture in hydroponics caused an increase of 107%, 197%, and 25% in the shoot length, total root length, and main root thickness respectively. The LAD treatment also significantly affected the rhizosphere microbial abundance and community structure. The rhizobacterial abundance and species richness in the corn seedlings treated with LAD culture were significantly lower than those in the control group. However, the LAD-treated samples had higher relative abundances of plant growth-promoting rhizobacteria like Bacillus and Burkholderia than the control samples did, suggesting that LAD treatment may facilitate the mutualistic relation between the rhizosphere microbiome and the plant. CONCLUSION These results collectively demonstrated that LAD is capable of shaping the rhizosphere microbial community structure and functions as a plant growth-promoting agent, which makes it a strong candidate for application as bio-fertilizer in agricultural systems. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Chao Deng
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Ning Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Xiaolong Liang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Tao Huang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - Bingxue Li
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
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Beale DJ, Shah RM, Marcora A, Hulthen A, Karpe AV, Pham K, Wijffels G, Paull C. Is there any biological insight (or respite) for insects exposed to plastics? Measuring the impact on an insects central carbon metabolism when exposed to a plastic feed substrate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 831:154840. [PMID: 35367264 DOI: 10.1016/j.scitotenv.2022.154840] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Insects used to treat organic waste streams and produce valuable protein products are increasingly exposed to plastic contaminated source material assimilating plastic carbon into organic biomass, which is pervasive and hazardous to organisms. Our understanding of this increased insect-plastic interaction remains limited and needs urgent scientific attention if plastic biodegradation and production rates of quality protein are to be improved. Herein, we investigated the biochemical impact of various plastics using three insect models. Black Soldier Fly (BSF), Mealworm (MW), and Wax Moth (WM) larva were each exposed to a plastic substrate (PET, PE, PS, Expanded PE, PP, and PLA) as the primary carbon source for five days to explore any positive metabolic benefits in terms of insect performance and plastic degradation potential. Central carbon metabolism (CCM) metabolites were analyzed via a targeted tMRM liquid chromatography triple quadrupole mass spectrometry (LC-QqQ-MS) method. Unique expressed pathways were observed for each insect model. When reared on PET, BSF larvae were found to have an elevated pyrimidine metabolism, while the purine metabolism pathway was strongly expressed on other plastics. BSF also exhibited a downregulated Vitamin B6 metabolism across all plastics, indicating a likely gut-symbiont breakdown. The MW and WM model insects were metabolically more active on PLA and expanded foam plastics. Further, WM exhibited an elevation in Vitamin B6 metabolism. This data suggests a positive insect-specific interaction towards certain plastic types that warrants further investigation. It is anticipated that through deeper insight into the metabolic impact and benefits afforded from certain plastics, an insect biotransformation pipeline can be established that links fit-for-purpose insect models to individual plastic types that address our growing plastic waste issue.
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Affiliation(s)
- David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, QLD 4102, Australia.
| | - Rohan M Shah
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Anna Marcora
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Andrew Hulthen
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Avinash V Karpe
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Khoa Pham
- CSIRO Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Clayton, VIC 4067, Australia
| | - Gene Wijffels
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Cate Paull
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
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Garber AI, Kupper M, Laetsch DR, Weldon SR, Ladinsky MS, Bjorkman PJ, McCutcheon JP. The Evolution of Interdependence in a Four-Way Mealybug Symbiosis. Genome Biol Evol 2021; 13:evab123. [PMID: 34061185 PMCID: PMC8331144 DOI: 10.1093/gbe/evab123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 01/03/2023] Open
Abstract
Mealybugs are insects that maintain intracellular bacterial symbionts to supplement their nutrient-poor plant sap diets. Some mealybugs have a single betaproteobacterial endosymbiont, a Candidatus Tremblaya species (hereafter Tremblaya) that alone provides the insect with its required nutrients. Other mealybugs have two nutritional endosymbionts that together provision these same nutrients, where Tremblaya has gained a gammaproteobacterial partner that resides in its cytoplasm. Previous work had established that Pseudococcus longispinus mealybugs maintain not one but two species of gammaproteobacterial endosymbionts along with Tremblaya. Preliminary genomic analyses suggested that these two gammaproteobacterial endosymbionts have large genomes with features consistent with a relatively recent origin as insect endosymbionts, but the patterns of genomic complementarity between members of the symbiosis and their relative cellular locations were unknown. Here, using long-read sequencing and various types of microscopy, we show that the two gammaproteobacterial symbionts of P. longispinus are mixed together within Tremblaya cells, and that their genomes are somewhat reduced in size compared with their closest nonendosymbiotic relatives. Both gammaproteobacterial genomes contain thousands of pseudogenes, consistent with a relatively recent shift from a free-living to an endosymbiotic lifestyle. Biosynthetic pathways of key metabolites are partitioned in complex interdependent patterns among the two gammaproteobacterial genomes, the Tremblaya genome, and horizontally acquired bacterial genes that are encoded on the mealybug nuclear genome. Although these two gammaproteobacterial endosymbionts have been acquired recently in evolutionary time, they have already evolved codependencies with each other, Tremblaya, and their insect host.
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Affiliation(s)
- Arkadiy I Garber
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Maria Kupper
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephanie R Weldon
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Mark S Ladinsky
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Pamela J Bjorkman
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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Petersen JM, Yuen B. The symbiotic 'all-rounders': Partnerships between marine animals and chemosynthetic nitrogen-fixing bacteria. Appl Environ Microbiol 2021; 87:AEM.02129-20. [PMID: 33355107 PMCID: PMC8090883 DOI: 10.1128/aem.02129-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrogen fixation is a widespread metabolic trait in certain types of microorganisms called diazotrophs. Bioavailable nitrogen is limited in various habitats on land and in the sea, and accordingly, a range of plant, animal, and single-celled eukaryotes have evolved symbioses with diverse diazotrophic bacteria, with enormous economic and ecological benefits. Until recently, all known nitrogen-fixing symbionts were heterotrophs such as nodulating rhizobia, or photoautotrophs such as cyanobacteria. In 2016, the first chemoautotrophic nitrogen-fixing symbionts were discovered in a common family of marine clams, the Lucinidae. Chemosynthetic nitrogen-fixing symbionts use the chemical energy stored in reduced sulfur compounds to power carbon and nitrogen fixation, making them metabolic 'all-rounders' with multiple functions in the symbiosis. This distinguishes them from heterotrophic symbionts that require a source of carbon from their host, and their chemosynthetic metabolism distinguishes them from photoautotrophic symbionts that produce oxygen, a potent inhibitor of nitrogenase. In this review, we consider evolutionary aspects of this discovery, by comparing strategies that have evolved for hosting intracellular nitrogen-fixing symbionts in plants and animals. The symbiosis between lucinid clams and chemosynthetic nitrogen-fixing bacteria also has important ecological impacts, as they form a nested symbiosis with endangered marine seagrasses. Notably, nitrogen fixation by lucinid symbionts may help support seagrass health by providing a source of nitrogen in seagrass habitats. These discoveries were enabled by new techniques for understanding the activity of microbial populations in natural environments. However, an animal (or plant) host represents a diverse landscape of microbial niches due to its structural, chemical, immune and behavioural properties. In future, methods that resolve microbial activity at the single cell level will provide radical new insights into the regulation of nitrogen fixation in chemosynthetic symbionts, shedding new light on the evolution of nitrogen-fixing symbioses in contrasting hosts and environments.
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Affiliation(s)
- Jillian M Petersen
- Centre for Microbiology and Environmental Systems Science, University of Vienna
| | - Benedict Yuen
- Centre for Microbiology and Environmental Systems Science, University of Vienna
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Hinzke T, Kleiner M, Meister M, Schlüter R, Hentschker C, Pané-Farré J, Hildebrandt P, Felbeck H, Sievert SM, Bonn F, Völker U, Becher D, Schweder T, Markert S. Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis. eLife 2021; 10:58371. [PMID: 33404502 PMCID: PMC7787665 DOI: 10.7554/elife.58371] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 12/05/2020] [Indexed: 12/13/2022] Open
Abstract
The hydrothermal vent tubeworm Riftia pachyptila hosts a single 16S rRNA phylotype of intracellular sulfur-oxidizing symbionts, which vary considerably in cell morphology and exhibit a remarkable degree of physiological diversity and redundancy, even in the same host. To elucidate whether multiple metabolic routes are employed in the same cells or rather in distinct symbiont subpopulations, we enriched symbionts according to cell size by density gradient centrifugation. Metaproteomic analysis, microscopy, and flow cytometry strongly suggest that Riftia symbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process: While small symbionts actively divide and may establish cellular symbiont-host interaction, large symbionts apparently do not divide, but still replicate DNA, leading to DNA endoreduplication. Moreover, in large symbionts, carbon fixation and biomass production seem to be metabolic priorities. We propose that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole.
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Affiliation(s)
- Tjorven Hinzke
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany.,Energy Bioengineering Group, University of Calgary, Calgary, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
| | - Mareike Meister
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.,Leibniz Institute for Plasma Science and Technology, Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Greifswald, Germany
| | - Christian Hentschker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jan Pané-Farré
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Petra Hildebrandt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Horst Felbeck
- Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, United States
| | - Florian Bonn
- Institute of Biochemistry, University Hospital, Goethe University School of Medicine Frankfurt, Frankfurt, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Stephanie Markert
- Institute of Pharmacy, University of Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
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