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Pitting the olive seed microbiome Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-03-15 Nuria M. Wentzien, Antonio J. Fernández-González, Antonio Valverde-Corredor, Ana V. Lasa, Pablo J. Villadas, Wisnu Adi Wicaksono, Tomislav Cernava, Gabriele Berg, Manuel Fernández-López, Jesús Mercado-Blanco
The complex and co-evolved interplay between plants and their microbiota is crucial for the health and fitness of the plant holobiont. However, the microbiota of the seeds is still relatively unexplored and no studies have been conducted with olive trees so far. In this study, we aimed to characterize the bacterial, fungal and archaeal communities present in seeds of ten olive genotypes growing in
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City-scale monitoring of antibiotic resistance genes by digital PCR and metagenomics Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-03-15 Lucia Maestre-Carballa, Vicente Navarro-López, Manuel Martinez-Garcia
Anthropogenic activities significantly contribute to the dissemination of antibiotic resistance genes (ARGs), posing a substantial threat to humankind. The development of methods that allow robust ARG surveillance is a long-standing challenge. Here, we use city-scale monitoring of ARGs by using two of the most promising cutting-edge technologies, digital PCR (dPCR) and metagenomics. ARG hot-spots were
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Microbiome changes through the ontogeny of the marine sponge Crambe crambe Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-03-11 Marta Turon, Madeline Ford, Manuel Maldonado, Cèlia Sitjà, Ana Riesgo, Cristina Díez-Vives
Poriferans (sponges) are highly adaptable organisms that can thrive in diverse marine and freshwater environments due, in part, to their close associations with internal microbial communities. This sponge microbiome can be acquired from the surrounding environment (horizontal acquisition) or obtained from the parents during the reproductive process through a variety of mechanisms (vertical transfer)
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Core hyphosphere microbiota of Fusarium oxysporum f. sp. niveum Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-03-09 Vanessa E. Thomas, Sanjay Antony-Babu
Bacteria and fungi are dynamically interconnected, leading to beneficial or antagonistic relationships with plants. Within this interkingdom interaction, the microbial community directly associated with the pathogen make up the pathobiome. While the overall soil bacterial community associated with Fusarium wilt diseases has been widely examined, the specific bacterial populations that directly interact
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Niche differentiation and biogeography of Bathyarchaeia in paddy soil ecosystems: a case study in eastern China Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-03-01 Xingyun Yi, Kristian Koefoed Brandt, Shudan Xue, Jingjing Peng, Yifei Wang, Meng Li, Ye Deng, Guilan Duan
Bathyarchaeia (formerly Bathyarchaeota) is a group of highly abundant archaeal communities that play important roles in global biogeochemical cycling. Bathyarchaeia is predominantly found in sediments and hot springs. However, their presence in arable soils is relatively limited. In this study, we aimed to investigate the spatial distributions and diversity of Bathyarchaeia in paddy soils across eastern
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Seed tuber imprinting shapes the next-generation potato microbiome Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-02-21 Yang Song, Jelle Spooren, Casper D. Jongekrijg, Ellen J. H. H. Manders, Ronnie de Jonge, Corné M. J. Pieterse, Peter A. H. M. Bakker, Roeland L. Berendsen
Potato seed tubers are colonized and inhabited by soil-borne microbes, that can affect the performance of the emerging daughter plant in the next season. In this study, we investigated the intergenerational inheritance of microbiota from seed tubers to next-season daughter plants under field condition by amplicon sequencing of bacterial and fungal microbiota associated with tubers and roots, and tracked
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The seeds of Plantago lanceolata comprise a stable core microbiome along a plant richness gradient Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-02-02 Yuri Pinheiro Alves de Souza, Michael Schloter, Wolfgang Weisser, Yuanyuan Huang, Stefanie Schulz
Seed endophytic bacteria are beneficial to plants. They improve seedling growth by enhancing plant nutrient uptake, modulating stress-related phytohormone production, and targeting pests and pathogens with antibiotics. Seed endophyte composition can be influenced by pollination, plant cultivar, and soil physicochemical conditions. However, the effects of plant community richness on seed endophytes
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Subtropical coastal microbiome variations due to massive river runoff after a cyclonic event Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-01-30 M. Meyneng, H. Lemonnier, R. Le Gendre, G. Plougoulen, F. Antypas, D. Ansquer, J. Serghine, S. Schmitt, R. Siano
Coastal ecosystem variability at tropical latitudes is dependent on climatic conditions. During the wet, rainy season, extreme climatic events such as cyclones, precipitation, and winds can be intense over a short period and may have a significant impact on the entire land‒sea continuum. This study focused on the effect of river runoff across the southwest coral lagoon ecosystem of Grand Terre Island
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Exploring virus-host-environment interactions in a chemotrophic-based underground estuary Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-01-30 Timothy M. Ghaly, Amaranta Focardi, Liam D. H. Elbourne, Brodie Sutcliffe, William F. Humphreys, Paul R. Jaschke, Sasha G. Tetu, Ian T. Paulsen
Viruses play important roles in modulating microbial communities and influencing global biogeochemistry. There is now growing interest in characterising their ecological roles across diverse biomes. However, little is known about viral ecology in low-nutrient, chemotrophic-based environments. In such ecosystems, virus-driven manipulation of nutrient cycles might have profound impacts across trophic
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Plant effects on microbiome composition are constrained by environmental conditions in a successional grassland Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-01-24 Lenka Mészárošová, Eliška Kuťáková, Petr Kohout, Zuzana Münzbergová, Petr Baldrian
Below-ground microbes mediate key ecosystem processes and play a vital role in plant nutrition and health. Understanding the composition of the belowground microbiome is therefore important for maintaining ecosystem stability. The structure of the belowground microbiome is largely determined by individual plants, but it is not clear how far their influence extends and, conversely, what the influence
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Weather in two climatic regions shapes the diversity and drives the structure of fungal endophytic community of bilberry (Vaccinium myrtillus L.) fruit Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-01-22 Minh-Phuong Nguyen, Kaisa Lehosmaa, Katalin Toth, Janne J. Koskimäki, Hely Häggman, Anna Maria Pirttilä
Bilberry (Vaccinium myrtillus L.) is one of the most important economic and natural resources in Northern Europe. Despite its importance, the endophytic fungal community of the fruits has rarely been investigated. Biogeographic patterns and determinants of the fungal diversity in the bilberry fruit are poorly understood, albeit fungal endophytes can have a close relationship with the host plants. Here
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Bacterial wilt affects the structure and assembly of microbial communities along the soil-root continuum Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-01-16 Jinchang Liang, Chengjian Wei, Xueru Song, Rui Wang, Heli Shi, Jun Tan, Dejie Cheng, Wenjing Wang, Xiaoqiang Wang
Beneficial root-associated microbiomes play crucial roles in enhancing plant growth and suppressing pathogenic threats, and their application for defending against pathogens has garnered increasing attention. Nonetheless, the dynamics of microbiome assembly and defense mechanisms during pathogen invasion remain largely unknown. In this study, we aimed to investigate the diversity and assembly of microbial
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The road forward to incorporate seawater microbes in predictive reef monitoring Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-01-15 Marko Terzin, Patrick W. Laffy, Steven Robbins, Yun Kit Yeoh, Pedro R. Frade, Bettina Glasl, Nicole S. Webster, David G. Bourne
Marine bacterioplankton underpin the health and function of coral reefs and respond in a rapid and sensitive manner to environmental changes that affect reef ecosystem stability. Numerous meta-omics surveys over recent years have documented persistent associations of opportunistic seawater microbial taxa, and their associated functions, with metrics of environmental stress and poor reef health (e.g
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Identification of potential microbial risk factors associated with fecal indicator exceedances at recreational beaches Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-01-15 Faizan Saleem, Enze Li, Thomas A. Edge, Kevin L. Tran, Herb E. Schellhorn
Fecal bacterial densities are proxy indicators of beach water quality, and beach posting decisions are made based on Beach Action Value (BAV) exceedances for a beach. However, these traditional beach monitoring methods do not reflect the full extent of microbial water quality changes associated with BAV exceedances at recreational beaches (including harmful cyanobacteria). This proof of concept study
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Phytoplankton ecology in the early years of a boreal oil sands end pit lake Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-01-12 Chantel C. Furgason, Angela V. Smirnova, Joel B. Dacks, Peter F. Dunfield
Base Mine Lake (BML) is the first full-scale end pit lake for the oil sands mining industry in Canada. BML sequesters oil sands tailings under a freshwater cap and is intended to develop into a functional ecosystem that can be integrated into the local watershed. The first stage of successful reclamation requires the development of a phytoplankton community supporting a typical boreal lake food web
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Selective regulation of endophytic bacteria and gene expression in soybean by water-soluble humic materials Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-01-04 Wenqian Wang, Dongmei Li, Xiaoqian Qiu, Jinshui Yang, Liang Liu, Entao Wang, Hongli Yuan
As part of the plant microbiome, endophytic bacteria play an essential role in plant growth and resistance to stress. Water-soluble humic materials (WSHM) is widely used in sustainable agriculture as a natural and non-polluting plant growth regulator to promote the growth of plants and beneficial bacteria. However, the mechanisms of WSHM to promote plant growth and the evidence for commensal endophytic
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A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes Stand. Genomic. Sci. (IF 7.9) Pub Date : 2024-01-02 Victor Borin Centurion, Alessandro Rossi, Esteban Orellana, Gabriele Ghiotto, Balázs Kakuk, Maria Silvia Morlino, Arianna Basile, Guido Zampieri, Laura Treu, Stefano Campanaro
The anaerobic digestion process degrades organic matter into simpler compounds and occurs in strictly anaerobic and microaerophilic environments. The process is carried out by a diverse community of microorganisms where each species has a unique role and it has relevant biotechnological applications since it is used for biogas production. Some aspects of the microbiome, including its interaction with
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Increased prokaryotic diversity in the Red Sea deep scattering layer Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-12-14 Tamara Megan Huete-Stauffer, Ramiro Logares, Mohd Ikram Ansari, Anders Røstad, Maria Lluch Calleja, Xosé Anxelu G. Morán
The diel vertical migration (DVM) of fish provides an active transport of labile dissolved organic matter (DOM) to the deep ocean, fueling the metabolism of heterotrophic bacteria and archaea. We studied the impact of DVM on the mesopelagic prokaryotic diversity of the Red Sea focusing on the mesopelagic deep scattering layer (DSL) between 450–600 m. Despite the general consensus of homogeneous conditions
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DNA from non-viable bacteria biases diversity estimates in the corals Acropora loripes and Pocillopora acuta Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-12-08 Ashley M. Dungan, Laura Geissler, Amanda S. Williams, Cecilie Ravn Gotze, Emily C. Flynn, Linda L. Blackall, Madeleine J. H. van Oppen
Nucleic acid-based analytical methods have greatly expanded our understanding of global prokaryotic diversity, yet standard metabarcoding methods provide no information on the most fundamental physiological state of bacteria, viability. Scleractinian corals harbour a complex microbiome in which bacterial symbionts play critical roles in maintaining health and functioning of the holobiont. However,
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Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-12-05 Lilian S. Abreu Soares Costa, Mírian Rabelo de Faria, Josiane Barros Chiaramonte, Lucas W. Mendes, Edis Sepo, Mattias de Hollander, José Maurício Cunha Fernandes, Víctor J. Carrión, Wagner Bettiol, Tim H. Mauchline, Jos M. Raaijmakers, Rodrigo Mendes
Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen. The results showed
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Grapevine bacterial communities display compartment-specific dynamics over space and time within the Central Valley of California Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-11-23 Joel F. Swift, Zoë Migicovsky, Grace E. Trello, Allison J. Miller
Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences along with microbial differences across sites compose
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A coral-associated actinobacterium mitigates coral bleaching under heat stress Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-11-23 Jie Li, Yiyang Zou, Qiqi Li, Jian Zhang, David G. Bourne, Yuanjiao Lyu, Cong Liu, Si Zhang
The positive effects of exposing corals to microorganisms have been reported though how the benefits are conferred are poorly understood. Here, we isolated an actinobacterial strain (SCSIO 13291) from Pocillopora damicornis with capabilities to synthesize antioxidants, vitamins, and antibacterial and antiviral compounds supported with phenotypic and/or genomic evidence. Strain SCSIO 13291 was labeled
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Microbial tapestry of the Shulgan-Tash cave (Southern Ural, Russia): influences of environmental factors on the taxonomic composition of the cave biofilms Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-11-21 Natalia Gogoleva, Olga Chervyatsova, Alexander Balkin, Lyudmila Kuzmina, Elena Shagimardanova, Daria Kiseleva, Yuri Gogolev
Cave biotopes are characterized by stable low temperatures, high humidity, and scarcity of organic substrates. Despite the harsh oligotrophic conditions, they are often inhabited by rich microbial communities. Abundant fouling with a wide range of morphology and coloration of colonies covers the walls of the Shulgan-Tash cave in the Southern Urals. This cave is also famous for the unique Paleolithic
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Designing a synthetic microbial community through genome metabolic modeling to enhance plant–microbe interaction Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-11-16 Osiel S. Gonçalves, Christopher J. Creevey, Mateus F. Santana
Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynComs, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and
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The gut microbiome mediates adaptation to scarce food in Coleoptera Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-11-13 Oana Teodora Moldovan, Alyssa A. Carrell, Paul-Adrian Bulzu, Erika Levei, Ruxandra Bucur, Cristian Sitar, Luchiana Faur, Ionuț Cornel Mirea, Marin Șenilă, Oana Cadar, Mircea Podar
Beetles are ubiquitous cave invertebrates worldwide that adapted to scarce subterranean resources when they colonized caves. Here, we investigated the potential role of gut microbiota in the adaptation of beetles to caves from different climatic regions of the Carpathians. The beetles’ microbiota was host-specific, reflecting phylogenetic and nutritional adaptation. The microbial community structure
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Exploring the influence of climatic variables on mycobiome composition and community diversity in lichens: insights from structural equation modeling analysis Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-10-27 Jiho Yang, Jung-Jae Woo, Wonyong Kim, Seung-Yoon Oh, Jae-Seoun Hur
Lichens are symbiotic organisms composed of a fungus and a photosynthetic partner, which are key ecological bioindicators due to their sensitivity to environmental changes. The endolichenic fungi (ELF) living inside lichen thalli, are an important but understudied component of playing crucial ecological roles such as nutrient cycling and protection against environmental stressors. Therefore ELF community
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Exploration of phyllosphere microbiomes in wheat varieties with differing aphid resistance Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-10-24 Xinan Li, Chao Wang, Xun Zhu, Vardis Ntoukakis, Tomislav Cernava, Decai Jin
Leaf-associated microbes play an important role in plant development and response to exogenous stress. Insect herbivores are known to alter the phyllosphere microbiome. However, whether the host plant’s defense against insects is related to the phyllosphere microbiome remains mostly elusive. Here, we investigated bacterial communities in the phyllosphere and endosphere of eight wheat cultivars with
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Distinct coral environments shape the dynamic of planktonic Vibrio spp. Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-10-23 Wenbin Zhao, Xing Chen, Ronghua Liu, Peng Tian, Wentao Niu, Xiao-Hua Zhang, Jiwen Liu, Xiaolei Wang
Coral reefs are one of the most biodiverse and productive ecosystems, providing habitat for a vast of species. Reef-building scleractinian corals with a symbiotic microbiome, including bacteria, archaea, viruses and eukaryotic microbes, are referred to coral holobionts. Among them, coral diseases, mainly caused by Vibrio spp., have significantly contributed to the loss of coral cover and diversity
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Successional action of Bacteroidota and Firmicutes in decomposing straw polymers in a paddy soil Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-10-14 Junjie Huang, Kailin Gao, Lu Yang, Yahai Lu
Decomposition of plant biomass is vital for carbon cycling in terrestrial ecosystems. In waterlogged soils including paddy fields and natural wetlands, plant biomass degradation generates the largest natural source of global methane emission. However, the intricate process of plant biomass degradation by diverse soil microorganisms remains poorly characterized. Here we report a chemical and metagenomic
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Distinct patterns of distribution, community assembly and cross-domain co-occurrence of planktonic archaea in four major estuaries of China Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-10-07 Xuya Hu, Yujie Huang, Gaoke Gu, Hanjing Hu, Huizhen Yan, Huajun Zhang, Rui Zhang, Demin Zhang, Kai Wang
Archaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling periods are scarce. Here, we investigated the distribution, community assembly, and cross-domain microbial co-occurrence of archaea in surface waters across four major estuaries (Yellow River, Yangtze
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Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-10-07 Martina Kracmarova-Farren, Jakub Papik, Ondrej Uhlik, John Freeman, Andrea Foster, Mary-Cathrine Leewis, Courtney Creamer
Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula, and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated
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Fungal community inside lichen: a curious case of sparse diversity and high modularity Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-10-03 Jiho Yang, Jung-Jae Woo, Seung-Yoon Oh, Wonyong Kim, Jae-Seoun Hur
Lichens represent not only the mutualism of fungal and photosynthetic partners but also are composed of microbial consortium harboring diverse fungi known as endolichenic fungi. While endolichenic fungi are known to exert a remarkable influence on lichen ecology through their crucial roles in nutrient cycling, bioprospecting and biodiversity, the enigmatic community structures of these fungal inhabitants
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Thiothrix and Sulfurovum genera dominate bacterial mats in Slovak cold sulfur springs Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-09-20 Lea Nosalova, Chahrazed Mekadim, Jakub Mrazek, Peter Pristas
Microbiota of sulfur-rich environments has been extensively studied due to the biotechnological potential of sulfur bacteria, or as a model of ancient life. Cold terrestrial sulfur springs are less studied compared to sulfur-oxidizing microbiota of hydrothermal vents, volcanic environments, or soda lakes. Despite that, several studies suggested that sulfur springs harbor diverse microbial communities
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Soil bacterial community composition is more stable in kiwifruit orchards relative to phyllosphere communities over time Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-08-24 Ziva Louisson, Louis Ranjard, Hannah L. Buckley, Bradley S. Case, Gavin Lear
Soil and phyllosphere (leaves and fruit) microbes play critical roles in the productivity and health of crops. However, microbial community dynamics are currently understudied in orchards, with a limited number incorporating temporal monitoring. We used 16S rRNA gene amplicon sequencing to investigate bacterial community temporal dynamics and community assembly processes on the leaves and fruit, and
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Holobiont responses of mesophotic precious red coral Corallium rubrum to thermal anomalies Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-08-14 Romie Tignat-Perrier, Jeroen A. J. M. van de Water, Denis Allemand, Christine Ferrier-Pagès
Marine heat waves (MHWs) have increased in frequency and intensity worldwide, causing mass mortality of benthic organisms and loss of biodiversity in shallow waters. The Mediterranean Sea is no exception, with shallow populations of habitat-forming octocorals facing the threat of local extinction. The mesophotic zone, which is less affected by MHWs, may be of ecological importance in conservation strategies
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Effects of marine sediment as agricultural substrate on soil microbial diversity: an amplicon sequencing study Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-08-07 Dámaris Núñez-Gómez, Pablo Melgarejo, Juan José Martínez-Nicolás, Francisca Hernández, Rafael Martínez-Font, Vicente Lidón, Pilar Legua
The soil microbiota has a direct impact on plant development and other metabolic systems, such as the degradation of organic matter and the availability of microelements and metabolites. In the context of agricultural soils, microbial activity is crucial for maintaining soil health and productivity. Thus, the present study aimed to identify, characterize, and quantify the microbial communities of four
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Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-08-03 Lucas William Mendes, Jos M Raaijmakers, Mattias de Hollander, Edis Sepo, Ruth Gómez Expósito, Alisson Fernando Chiorato, Rodrigo Mendes, Siu Mui Tsai, Victor J Carrión
Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact
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Insights into the prokaryotic communities of the abyssal-hadal benthic-boundary layer of the Kuril Kamchatka Trench Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-08-02 Susanna Gorrasi, Andrea Franzetti, Angelika Brandt, Ulrike Minzlaff, Marcella Pasqualetti, Massimiliano Fenice
The Kuril–Kamchatka Trench (maximum depth 9604 m), located in the NW Pacific Ocean, is among the top seven deepest hadal trenches. The work aimed to investigate the unexplored abyssal-hadal prokaryotic communities of this fascinating, but underrated environment. As for the bacterial communities, we found that Proteobacteria (56.1–74.5%), Bacteroidetes (6.5–19.1%), and Actinobacteria (0.9–16.1%) were
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Meeting report of the sixth annual tri-service microbiome consortium symposium Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-08-02 Ida G. Pantoja-Feliciano De Goodfellow, Richard Agans, Robyn Barbato, Sophie Colston, Michael S. Goodson, Rasha Hammamieh, Kristy Hentchel, Robert Jones, J. Philip Karl, Robert Kokoska, Dagmar H. Leary, Camilla Mauzy, Kenneth Racicot, Blake W. Stamps, Vanessa Varaljay, Jason W. Soares
The Tri-Service Microbiome Consortium (TSMC) was founded to enhance collaboration, coordination, and communication of microbiome research among DoD organizations and to facilitate resource, material and information sharing amongst consortium members, which includes collaborators in academia and industry. The 6th Annual TSMC Symposium was a hybrid meeting held in Fairlee, Vermont on 27–28 September
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A symbiotic footprint in the plant root microbiome Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-07-31 Kyle Hartman, Marc W. Schmid, Natacha Bodenhausen, S. Franz Bender, Alain Y. Valzano-Held, Klaus Schlaeppi, Marcel G.A. van der Heijden
A major aim in plant microbiome research is determining the drivers of plant-associated microbial communities. While soil characteristics and host plant identity present key drivers of root microbiome composition, it is still unresolved whether the presence or absence of important plant root symbionts also determines overall microbiome composition. Arbuscular mycorrhizal fungi (AMF) and N-fixing rhizobia
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Microbiome specificity and fluxes between two distant plant taxa in Iberian forests Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-07-22 Zaki Saati-Santamaría, Rocío Vicentefranqueira, Miroslav Kolařik, Raúl Rivas, Paula García-Fraile
Plant-associated microbial communities play important roles in host nutrition, development and defence. In particular, the microbes living within internal plant tissues can affect plant metabolism in a more intimate way. Understanding the factors that shape plant microbial composition and discovering enriched microbes within endophytic compartments would thus be valuable to gain knowledge on potential
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Reciprocal influence of soil, phyllosphere, and aphid microbiomes Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-07-21 Adrian Wolfgang, Ayco J. M. Tack, Gabriele Berg, Ahmed Abdelfattah
The effect of soil on the plant microbiome is well-studied. However, less is known about the impact of the soil microbiome in multitrophic systems. Here we examined the effect of soil on plant and aphid microbiomes, and the reciprocal effect of aphid herbivory on the plant and soil microbiomes. We designed microcosms, which separate below and aboveground compartments, to grow oak seedlings with and
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Pioneer Arabidopsis thaliana spans the succession gradient revealing a diverse root-associated microbiome Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-07-19 Vera Hesen, Yvet Boele, Tanja Bakx-Schotman, Femke van Beersum, Ciska Raaijmakers, Ben Scheres, Viola Willemsen, Wim H. van der Putten
Soil microbiomes are increasingly acknowledged to affect plant functioning. Research in molecular model species Arabidopsis thaliana has given detailed insights of such plant-microbiome interactions. However, the circumstances under which natural A. thaliana plants have been studied so far might represent only a subset of A. thaliana’s full ecological context and potential biotic diversity of its root-associated
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Evolutionary patterns of archaea predominant in acidic environment Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-07-18 Rafael Bargiela, Aleksei A. Korzhenkov, Owen A. McIntosh, Stepan V. Toshchakov, Mikhail M. Yakimov, Peter N. Golyshin, Olga V. Golyshina
Archaea of the order Thermoplasmatales are widely distributed in natural acidic areas and are amongst the most acidophilic prokaryotic organisms known so far. These organisms are difficult to culture, with currently only six genera validly published since the discovery of Thermoplasma acidophilum in 1970. Moreover, known great diversity of uncultured Thermoplasmatales represents microbial dark matter
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Elucidating the effects of organic vs. conventional cropping practice and rhizobia inoculation on rhizosphere microbial diversity and yield of peanut Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-07-18 Dev Paudel, Liping Wang, Ravin Poudel, Janam P Acharya, Samantha Victores, Cleber Henrique Lopes de Souza, Esteban Rios, Jianping Wang
Legumes such as peanut (Arachis hypogea) can fulfill most of their nitrogen requirement by symbiotic association with nitrogen-fixing bacteria, rhizobia. Nutrient availability is largely determined by microbial diversity and activity in the rhizosphere that influences plant health, nutrition, and crop yield, as well as soil quality and soil fertility. However, our understanding of the complex effects
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Assembly processes and functional diversity of marine protists and their rare biosphere Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-07-13 Pierre Ramond, Raffaele Siano, Marc Sourisseau, Ramiro Logares
The mechanisms shaping the rare microbial biosphere and its role in ecosystems remain unclear. We developed an approach to study ecological patterns in the rare biosphere and use it on a vast collection of marine microbiomes, sampled in coastal ecosystems at a regional scale. We study the assembly processes, and the ecological strategies constituting the rare protistan biosphere. Using the phylogeny
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Dynamic of active microbial diversity in rhizosphere sediments of halophytes used for bioremediation of earthen shrimp ponds Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-07-12 Marie Colette, Linda Guentas, Luc Della Patrona, Dominique Ansquer, Nolwenn Callac
In New-Caledonia, at the end of each shrimp production cycle, earthen ponds are drained and dried to enhance microbial decomposition of nutrient-rich waste trapped in the sediment during the rearing. However, excessive ponds drying may not be suitable for the decomposition activities of microorganisms. Halophytes, salt tolerant plants, naturally grow at vicinity of shrimp ponds; due to their specificity
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Modules in robust but low-efficiency phyllosphere fungal networks drive saponin accumulation in leaves of different Panax species Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-07-12 Guozhuang Zhang, Liping Shi, Congsheng Liu, Renjun Mao, Bing Xia, Zhixin Huang, Xiuye Wei, Lixuan Wu, Yuqing Zheng, Guangfei Wei, Jia Xu, Shuangrong Gao, Shilin Chen, Linlin Dong
The phyllosphere mycobiome plays a crucial role in plant fitness and ecosystem functions. The complex microbial ecological networks (MEN) formed by these fungi remain poorly understood, particularly with regard to their organization strategy and their contributions to plant secondary metabolites such as saponin. In this study, we constructed six MENs from leaf epiphytic and endophytic mycobiomes of
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Integrative meta-omics in Galaxy and beyond Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-07-07 Valerie C. Schiml, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin, Magnus Ø. Arntzen
‘Omics methods have empowered scientists to tackle the complexity of microbial communities on a scale not attainable before. Individually, omics analyses can provide great insight; while combined as “meta-omics”, they enhance the understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize environmental nutrients. Here we present three integrative meta-omics
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The microbial composition of larval airways from Drosophila melanogaster differ between specimens from laboratory and natural habitats Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-06-27 Hanna Angstmann, Stefan Pfeiffer, Susanne Kublik, Birte Ehrhardt, Karin Uliczka, Klaus F. Rabe, Thomas Roeder, Christina Wagner, Michael Schloter, Susanne Krauss-Etschmann
The fruit fly Drosophila melanogaster lives in natural habitats and has also long been used as a model organism in biological research. In this study, we used a molecular barcoding approach to analyse the airways microbiome of larvae of D. melanogaster, which were obtained from eggs of flies of the laboratory strain w1118 and from immune deficient flies (NF-kB-K), and from wild-caught flies. To assess
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Distinct taxonomic and functional profiles of high Arctic and alpine permafrost-affected soil microbiomes Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-06-16 Ciro Sannino, Weihong Qi, Joel Rüthi, Beat Stierli, Beat Frey
Global warming is affecting all cold environments, including the European Alps and Arctic regions. Here, permafrost may be considered a unique ecosystem harboring a distinct microbiome. The frequent freeze–thaw cycles occurring in permafrost-affected soils, and mainly in the seasonally active top layers, modify microbial communities and consequently ecosystem processes. Although taxonomic responses
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New insight into the bark beetle ips typographus bacteriome reveals unexplored diversity potentially beneficial to the host Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-06-09 Ezequiel Peral-Aranega, Zaki Saati-Santamaría, Miguel Ayuso-Calles, Martin Kostovčík, Tereza Veselská, Karel Švec, Raúl Rivas, Miroslav Kolařik, Paula García-Fraile
Ips typographus (European spruce bark beetle) is the most destructive pest of spruce forests in Europe. As for other animals, it has been proposed that the microbiome plays important roles in the biology of bark beetles. About the bacteriome, there still are many uncertainties regarding the taxonomical composition, insect-bacteriome interactions, and their potential roles in the beetle ecology. Here
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Microbiome species diversity and seasonal stability of two temperate marine sponges Hymeniacidon perlevis and Suberites massa Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-06-08 Claire E. Lamb, Joy E. M. Watts
Marine sponges are diverse and functionally important members of marine benthic systems, well known to harbour complex and abundant symbiotic microorganisms as part of their species-specific microbiome. Changes in the sponge microbiome have previously been observed in relation to natural environmental changes, including nutrient availability, temperature and light. With global climate change altering
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Correction to: Non contiguous-finished genome sequence and description of Bacillus timonensis sp. nov Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-06-07 Sahare Kokcha, Ajay Kumar Mishra, Jean-Christophe Lagier, Matthieu Million, Quentin Leroy, Didier Raoult, Pierre-Edouard Fournier
Correction: Standards in Genomic Sciences 20126:3 https://doi.org/10.4056/sigs.2776064. Following publication of the original article [1], the authors flagged the following errors: The original version of this article unfortunately contained two mistakes: (1) the authors had omitted to mention 10403188T as type strain name of the new species Bacillus timonensis (MM10403188T had been written instead)
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Regional biogeography versus intra-annual dynamics of the root and soil microbiome Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-06-07 Lukas P. Bell-Dereske, Gian Maria Niccolò Benucci, Pedro Beschoren da Costa, Gregory Bonito, Maren L. Friesen, Lisa K. Tiemann, Sarah E. Evans
Root and soil microbial communities constitute the below-ground plant microbiome, are drivers of nutrient cycling, and affect plant productivity. However, our understanding of their spatiotemporal patterns is confounded by exogenous factors that covary spatially, such as changes in host plant species, climate, and edaphic factors. These spatiotemporal patterns likely differ across microbiome domains
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The impacts of ocean acidification, warming and their interactive effects on coral prokaryotic symbionts Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-06-07 Jinlong Li, Guangjun Chai, Yilin Xiao, Zhiyong Li
Reef-building corals, the foundation of tropical coral reefs, are vulnerable to climate change e.g. ocean acidification and elevated seawater temperature. Coral microbiome plays a key role in host acclimatization and maintenance of the coral holobiont’s homeostasis under different environmental conditions, however, the response patterns of coral prokaryotic symbionts to ocean acidification and/or warming
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Variations in the archaeal community and associated methanogenesis in peat profiles of three typical peatland types in China Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-06-06 Xuhui Chen, Dan Xue, Yue Wang, Qing Qiu, Lin Wu, Meng Wang, Jiawen Liu, Huai Chen
Peatlands contain about 500 Pg of carbon worldwide and play a dual role as both a carbon sink and an important methane (CH4) source, thereby potentially influencing climate change. However, systematic studies on peat properties, microorganisms, methanogenesis, and their interrelations in peatlands remain limited, especially in China. Therefore, the present study aims to investigate the physicochemical
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The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-06-01 Benjamin J. Wainwright, Trevor Millar, Lacee Bowen, Lauren Semon, K. J. E. Hickman, Jen Nie Lee, Zhi Yi Yeo, Geoffrey Zahn
Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and if not for microbial cycling of nutrients, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse on the
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The microbiome of Riccia liverworts is an important reservoir for microbial diversity in temporary agricultural crusts Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-06-01 Wisnu Adi Wicaksono, Bettina Semler, Martina Pöltl, Christian Berg, Gabriele Berg, Tomislav Cernava
The microbiota of liverworts provides an interesting model for plant symbioses; however, their microbiome assembly is not yet understood. Here, we assessed specific factors that shape microbial communities associated with Riccia temporary agricultural crusts in harvested fields by investigating bacterial, fungal and archaeal communities in thalli and adhering soil from different field sites in Styria
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What matters most? Assessment of within-canopy factors influencing the needle microbiome of the model conifer, Pinus radiata Stand. Genomic. Sci. (IF 7.9) Pub Date : 2023-05-30 Sarah Addison, Charlotte Armstrong, Kathryn Wigley, Robin Hartley, Steven Wakelin
The assembly and function of the phyllosphere microbiome is important to the overall fitness of plants and, thereby, the ecosystems they inhabit. Presently, model systems for tree phyllosphere microbiome studies are lacking, yet forests resilient to pests, diseases, and climate change are important to support a myriad of ecosystem services impacting from local to global levels. In this study, we extend