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Efremova J, Mazzella V, Mirasole A, Teixidó N, Núñez-Pons L. Divergent morphological and microbiome strategies of two neighbor sponges to cope with low pH in Mediterranean CO 2 vents. Sci Total Environ 2024; 916:170171. [PMID: 38246375 DOI: 10.1016/j.scitotenv.2024.170171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/23/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
Ocean Acidification (OA) profoundly impacts marine biochemistry, resulting in a net loss of biodiversity. Porifera are often forecasted as winner taxa, yet the strategies to cope with OA can vary and may generate diverse fitness status. In this study, microbial shifts based on the V3-V4 16S rRNA gene marker were compared across neighboring Chondrosia reniformis sponges with high microbial abundance (HMA), and Spirastrella cunctatrix with low microbial abundance (LMA) microbiomes. Sponge holobionts co-occurred in a CO2 vent system with low pH (pHT ~ 7.65), and a control site with Ambient pH (pHT ~ 8.05) off Ischia Island, representing natural analogues to study future OA, and species' responses in the face of global environmental change. Microbial diversity and composition varied in both species across sites, yet at different levels. Increased numbers of core taxa were detected in S. cunctatrix, and a more diverse and flexible core microbiome was reported in C. reniformis under OA. Vent S. cunctatrix showed morphological impairment, along with signs of putative stress-induced dysbiosis, manifested by: 1) increases in alpha diversity, 2) shifts from sponge related microbes towards seawater microbes, and 3) high dysbiosis scores. Chondrosia reniformis in lieu, showed no morphological variation, low dysbiosis scores, and experienced a reduction in alpha diversity and less number of core taxa in vent specimens. Therefore, C. reniformis is hypothesized to maintain an state of normobiosis and acclimatize to OA, thanks to a more diverse, and likely metabolically versatile microbiome. A consortium of differentially abundant microbes was identified associated to either vent or control sponges, and chiefly related to carbon, nitrogen and sulfur-metabolisms for nutrient cycling and vitamin production, as well as probiotic symbionts in C. reniformis. Diversified symbiont associates supporting functional convergence could be the key behind resilience towards OA, yet specific acclimatization traits should be further investigated.
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Affiliation(s)
- Jana Efremova
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy.
| | - Valerio Mazzella
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy.
| | - Alice Mirasole
- Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy.
| | - Núria Teixidó
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy; Laboratoire d'Océanographie de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-mer, France.
| | - Laura Núñez-Pons
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy.
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Šigutová H, Pyszko P, Šigut M, Czajová K, Kostovčík M, Kolařík M, Hařovská D, Drozd P. Concentration-dependent effect of plant secondary metabolites on bacterial and fungal microbiomes in caterpillar guts. Microbiol Spectr 2024; 12:e0299423. [PMID: 37991377 PMCID: PMC10783044 DOI: 10.1128/spectrum.02994-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/16/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE The caterpillar gut is an excellent model system for studying host-microbiome interactions, as it represents an extreme environment for microbial life that usually has low diversity and considerable variability in community composition. Our study design combines feeding caterpillars on a natural and artificial diet with controlled levels of plant secondary metabolites and uses metabarcoding and quantitative PCR to simultaneously profile bacterial and fungal assemblages, which has never been performed. Moreover, we focus on multiple caterpillar species and consider diet breadth. Contrary to many previous studies, our study suggested the functional importance of certain microbial taxa, especially bacteria, and confirmed the previously proposed lower importance of fungi for caterpillar holobiont. Our study revealed the lack of differences between monophagous and polyphagous species in the responses of microbial assemblages to plant secondary metabolites, suggesting the limited role of the microbiome in the plasticity of the herbivore diet.
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Affiliation(s)
- Hana Šigutová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Department of Zoology, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Petr Pyszko
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Martin Šigut
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Kateřina Czajová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Martin Kostovčík
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Miroslav Kolařík
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Denisa Hařovská
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Pavel Drozd
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
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De Filippis F, Bonelli M, Bruno D, Sequino G, Montali A, Reguzzoni M, Pasolli E, Savy D, Cangemi S, Cozzolino V, Tettamanti G, Ercolini D, Casartelli M, Caccia S. Plastics shape the black soldier fly larvae gut microbiome and select for biodegrading functions. Microbiome 2023; 11:205. [PMID: 37705113 PMCID: PMC10500907 DOI: 10.1186/s40168-023-01649-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 07/16/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND In the last few years, considerable attention has been focused on the plastic-degrading capability of insects and their gut microbiota in order to develop novel, effective, and green strategies for plastic waste management. Although many analyses based on 16S rRNA gene sequencing are available, an in-depth analysis of the insect gut microbiome to identify genes with plastic-degrading potential is still lacking. RESULTS In the present work, we aim to fill this gap using Black Soldier Fly (BSF) as insect model. BSF larvae have proven capability to efficiently bioconvert a wide variety of organic wastes but, surprisingly, have never been considered for plastic degradation. BSF larvae were reared on two widely used plastic polymers and shotgun metagenomics was exploited to evaluate if and how plastic-containing diets affect composition and functions of the gut microbial community. The high-definition picture of the BSF gut microbiome gave access for the first time to the genomes of culturable and unculturable microorganisms in the gut of insects reared on plastics and revealed that (i) plastics significantly shaped bacterial composition at species and strain level, and (ii) functions that trigger the degradation of the polymer chains, i.e., DyP-type peroxidases, multicopper oxidases, and alkane monooxygenases, were highly enriched in the metagenomes upon exposure to plastics, consistently with the evidences obtained by scanning electron microscopy and 1H nuclear magnetic resonance analyses on plastics. CONCLUSIONS In addition to highlighting that the astonishing plasticity of the microbiota composition of BSF larvae is associated with functional shifts in the insect microbiome, the present work sets the stage for exploiting BSF larvae as "bioincubators" to isolate microbial strains and enzymes for the development of innovative plastic biodegradation strategies. However, most importantly, the larvae constitute a source of enzymes to be evolved and valorized by pioneering synthetic biology approaches. Video Abstract.
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Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Marco Bonelli
- Department of Biosciences, University of Milan, Milan, Italy
| | - Daniele Bruno
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Giuseppina Sequino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Aurora Montali
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Marcella Reguzzoni
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Davide Savy
- Interdepartmental Research Centre of Nuclear Magnetic Resonance for the Environment, Agri-Food and New Materials (CERMANU), University of Naples Federico II, Portici, Italy
| | - Silvana Cangemi
- Interdepartmental Research Centre of Nuclear Magnetic Resonance for the Environment, Agri-Food and New Materials (CERMANU), University of Naples Federico II, Portici, Italy
| | - Vincenza Cozzolino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Interdepartmental Research Centre of Nuclear Magnetic Resonance for the Environment, Agri-Food and New Materials (CERMANU), University of Naples Federico II, Portici, Italy
| | - Gianluca Tettamanti
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Portici, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
| | - Morena Casartelli
- Department of Biosciences, University of Milan, Milan, Italy.
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Portici, Italy.
| | - Silvia Caccia
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
- Department of Biosciences, University of Milan, Milan, Italy.
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Auger L, Deschamps MH, Vandenberg G, Derome N. Microbiota is structured by gut regions, life stage, and diet in the Black Soldier Fly ( Hermetia illucens). Front Microbiol 2023; 14:1221728. [PMID: 37664118 PMCID: PMC10469785 DOI: 10.3389/fmicb.2023.1221728] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/26/2023] [Indexed: 09/05/2023] Open
Abstract
The larvae of the Black Soldier Fly (Hermetia illucens) provide numerous ecological benefits, leading to significant commercial advancements. These benefits include the bioconversion of low-value waste into high-value feed and soil amendments. Understanding how the bacterial and eukaryotic microbiota communities affect host performance becomes vital for the optimization and specialization of industrial-scale rearing. This study investigates H. illucens-associated microbiota taxonomic composition and dynamics across the developmental cycle (eggs, neonates, larvae, prepupae, and imago X0 to second generation X1) when reared on two substrates: (i) plant-based (Housefly Gainesville diet) and (ii) animal-based (poultry hatchery waste). By using the 16S gene amplicon metataxonomic approach, we found that the results revealed that bacterial microbiota inherited from parents reared on a different substrate may have induced dysbiosis in the progeny. Specifically, the interaction networks of individuals reared on hatchery waste showed a high prevalence of negative interactions and low connectivity. Proteobacteria (39-92%), Firmicutes (4-39%), Bacteroidota (1-38%), and Actinobacteria (1-33%). In animal feed-reared individuals, Firmicutes reached the highest relative abundance (10-80%), followed by Proteobacteria (6-55%), Actinobacteria (1-31%), and Bacteroidota (0-22%). The rearing substrate was the main driver of microbiota composition, while the developmental stage influenced only the whole individual's bacterial microbiota composition. Gut regions were associated with distinct bacterial composition and richness, with diversity decreasing along the digestive tract. For the first time, microeukaryotes of the microbiota other than Fungi were investigated using 18S genetic marker amplicon sequencing with novel blocking primers specific to the Black Soldier Fly. Microeukaryotes are a neglected part of multitrophic microbiota communities that can have similar effects on their hosts as bacterial microbiota. Microeukaryotes from seven orders were identified in black soldier flies, including potential pathogens (e.g., Aplicomplexa group). Nucletmycea were the dominant class throughout development, followed by Holozoa and Stramenophiles. The eukaryote microbiota was structured by developmental stages but not by gut regions. Insights from this study are a stepping stone toward the microbiological optimization of black soldier flies for industrial rearing, highlighting how a synthetic microbiota assembly should be tailored to the rearing environment of the larvae at a targeted developmental stage.
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Affiliation(s)
- Laurence Auger
- Laboratory Derome, Département de Biologie, Institute of Integrative Biology and Systems, Université Laval, Québec, QC, Canada
| | | | - Grant Vandenberg
- Département des Sciences Animales, Université Laval, Québec, QC, Canada
| | - Nicolas Derome
- Laboratory Derome, Département de Biologie, Institute of Integrative Biology and Systems, Université Laval, Québec, QC, Canada
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Girard M, Luis P, Valiente Moro C, Minard G. Crosstalk between the microbiota and insect postembryonic development. Trends Microbiol 2023; 31:181-96. [PMID: 36167769 DOI: 10.1016/j.tim.2022.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/20/2022] [Accepted: 08/25/2022] [Indexed: 01/27/2023]
Abstract
Insect sequential development evolves from a simple molt towards complete metamorphosis. Like any multicellular host, insects interact with a complex microbiota. In this review, factors driving the microbiota dynamics were pointed out along their development. Special focus was put on tissue renewal, shift in insect ecology, and microbial interactions. Conversely, how the microbiota modulates its host development through nutrient acquisition, hormonal control, and cellular or tissue differentiation was exemplified. Such modifications might have long-term carry-over effects on insect physiology. Finally, remarkable microbe-driven control of insect behaviors along their life cycle was highlighted. Increasing knowledge of those interactions might offer new insights on how insects respond to their environment as well as perspectives on pest- or vector-control strategies.
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Perrotta BG, Kidd KA, Walters DM. PCB exposure is associated with reduction of endosymbionts in riparian spider microbiomes. Sci Total Environ 2022; 842:156726. [PMID: 35716742 DOI: 10.1016/j.scitotenv.2022.156726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/07/2022] [Accepted: 06/12/2022] [Indexed: 06/15/2023]
Abstract
Microbial communities, including endosymbionts, play diverse and critical roles in host biology and reproduction, but contaminant exposure may cause an imbalance in the microbiome composition with subsequent impacts on host health. Here, we examined whether there was a significant alteration of the microbiome community within two taxa of riparian spiders (Tetragnathidae and Araneidae) from a site with historical polychlorinated biphenyl (PCB) contamination in southern Ontario, Canada. Riparian spiders specialize in the predation of adult aquatic insects and, as such, their contaminant levels closely track those of nearby aquatic ecosystems. DNA from whole spiders from sites with either low or high PCB contamination was extracted, and spider microbiota profiled by partial 16S rRNA gene amplicon sequencing. The most prevalent shift in microbial communities we observed was a large reduction in endosymbionts in spiders at the high PCB site. The abundance of endosymbionts at the high PCB site was 63 % and 98 % lower for tetragnathids and araneids, respectively, than at the low PCB site. Overall, this has potential implications for spider reproductive success and food webs, as riparian spiders are critical gatekeepers of energy and material fluxes at the land-water interface.
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Affiliation(s)
- Brittany G Perrotta
- Department of Biology, McMaster University, Hamilton, Ontario, Canada; Contractor, U.S. Geological Survey, Columbia Environmental Research Center, Columbia, Missouri, USA
| | - Karen A Kidd
- Department of Biology, McMaster University, Hamilton, Ontario, Canada; School of Earth, Environment and Society, McMaster University, Hamilton, Ontario, Canada.
| | - David M Walters
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO, USA
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Kivistik C, Käiro K, Tammert H, Sokolova IM, Kisand V, Herlemann DPR. Distinct stages of the intestinal bacterial community of Ampullaceana balthica after salinization. Front Microbiol 2022; 13:767334. [PMID: 36110301 PMCID: PMC9468257 DOI: 10.3389/fmicb.2022.767334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 07/19/2022] [Indexed: 12/15/2022] Open
Abstract
Environmental disturbances influence bacterial community structure and functioning. To investigate the effect of environmental disturbance caused by changes in salinity on host-protected bacterial communities, we analyzed the microbiome within the gastrointestinal tract of Ampullaceana balthica in different salinities. A. balthica is a benthic gastropod found in fresh- and mesohaline waters. Whereas the total energy reserves of A. balthica were unaffected by an increase of salinity to 3, a high mortality rate was detected after a shift from freshwater to salinity 6 suggesting a major disruption of energy homeostasis. The shift to salinity 6 also caused a change in the gastrointestinal bacterial community composition. At salinity 3, the bacterial community composition of different host individuals was related either to the freshwater or salinity 6 gastrointestinal bacterial community, indicating an ambivalent nature of salinity 3. Since salinity 3 represents the range where aquatic gastropods are able to regulate their osmolarity, this may be an important tipping point during salinization. The change in the intestinal microbiome was uncoupled from the change in the water bacterial community and unrelated to the food source microbiome. Our study shows that environmental disturbance caused by salinity acts also on the host-protected microbiome. In light of the sea-level rise, our findings indicate that salinization of the near-shore freshwater bodies will cause changes in organisms' intestinal microbiomes if a critical salinity threshold (presumably ∼3) is exceeded.
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Affiliation(s)
- Carmen Kivistik
- Estonian University of Life Sciences, Center for Limnology, Tartu, Estonia
| | - Kairi Käiro
- Estonian University of Life Sciences, Center for Limnology, Tartu, Estonia
| | - Helen Tammert
- Estonian University of Life Sciences, Center for Limnology, Tartu, Estonia
| | - Inna M. Sokolova
- Department of Marine Biology, Institute for Biological Sciences, University of Rostock, Rostock, Germany
- Department of Maritime Systems, Interdisciplinary Faculty, University of Rostock, Rostock, Germany
| | - Veljo Kisand
- Estonian University of Life Sciences, Center for Limnology, Tartu, Estonia
- Institute of Technology, University of Tartu, Tartu, Estonia
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Mason CJ, Peiffer M, Felton GW, Hoover K. Host-Specific larval lepidopteran mortality to pathogenic Serratia mediated by poor diet. J Invertebr Pathol 2022; 194:107818. [PMID: 35973510 DOI: 10.1016/j.jip.2022.107818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/11/2022] [Accepted: 08/10/2022] [Indexed: 11/20/2022]
Abstract
Insect guts often harbor an abundance of bacteria. Many of these members are commensal, but some may emerge as opportunistic pathogens when the host is under stress. In this study, we evaluated how dietary nutritional concentration mediates a shift from commensal to pathogenic, and if host species influences those interactions. We used the lepidopterans (Noctuidae) fall armyworm (Spodoptera frugiperda), beet armyworm (Spodoptera exigua), and corn earworm (Helicoverpa zea) as hosts and a Serratia strain initially isolated from healthy fall armyworm. Diet concentration was altered by bulk reduction in nutritional content with dilution using cellulose. Our experiments revealed that low nutrient diet increased mortality from Serratia for beet armyworm and corn earworm. However, for fall armyworm, little mortality was observed in any of the diet combinations. Dietary nutrition and oral inoculation with Serratia did not change the expression of two antimicrobial peptides in fall and beet armyworm, suggesting that other mechanisms that mediate mortality were involved. Our results have implications for how pathogens may persist as commensals in the digestive tract of insects. These findings also suggest that diet plays a very important role in the switch from commensal to pathogen. Finally, our data indicate that the host response to changing conditions is critical in determining if a pathogen may overtake its host and that these three lepidopteran species have different responses to opportunistic enteric pathogens.
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