-
Global freshwater distribution of Telonemia protists. ISME J. (IF 10.8) Pub Date : 2024-09-20 Roudaina Boukheloua,Indranil Mukherjee,Hongjae Park,Karel Šimek,Vojtěch Kasalický,Maxon Ngochera,Hans-Peter Grossart,Antonio Picazo-Mozo,Antonio Camacho,Pedro J Cabello-Yeves,Francisco Rodriguez-Valera,Cristiana Callieri,Adrian-Stefan Andrei,Jakob Pernthaler,Thomas Posch,Albin Alfreider,Ruben Sommaruga,Martin W Hahn,Bettina Sonntag,Purificacion Lopez-Garcia,David Moreira,Ludwig Jardillier,Cécile Lepère
Telonemia are one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedis lineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predatory flagellate, especially in freshwater food webs
-
Drivers and consequences of microbial community coalescence ISME J. (IF 10.8) Pub Date : 2024-09-17 Xipeng Liu, Joana Falcão Salles
Microbial communities are undergoing unprecedented dispersion and amalgamation across diverse ecosystems, thereby exerting profound and pervasive influences on microbial assemblages and ecosystem dynamics. This review delves into the phenomenon of community coalescence, offering an ecological overview that outlines its four-step process and elucidates the intrinsic interconnections in the context of
-
Convergence of gut phage communities but not bacterial communities following wild mouse bacteriophage transplantation into captive house mice ISME J. (IF 10.8) Pub Date : 2024-09-14 Dagmar Čížková, Pavel Payne, Anna Bryjová, Ľudovít Ďureje, Jaroslav Piálek, Jakub Kreisinger
Bacteriophages are abundant components of vertebrate gut microbial communities, impacting bacteriome dynamics, evolution, and directly interacting with the superhost. However, knowledge about gut phageomes and their interaction with bacteriomes in vertebrates under natural conditions is limited to humans and non-human primates. Widely used specific pathogen-free (SPF) mouse models of host-microbiota
-
Chemolithoautotrophic bacteria flourish at dark water-ice interfaces of an emerged Arctic cold seep. ISME J. (IF 10.8) Pub Date : 2024-09-12 Lisa-Marie Delpech,Alexander T Tveit,Andrew J Hodson,Kevin P Hand,Dimitri Kalenitchenko
Below their ice shells, icy moons may offer a source of chemical energy that could support microbial life in the absence of light. In the Arctic, past and present glacial retreat leads to isostatic uplift of sediments through which cold and methane-saturated groundwater travels. This fluid reaches the surface and freezes as hill-shaped icings during winter, producing dark ice-water interfaces above
-
Oxidation of sulfur, hydrogen, and iron by metabolically versatile Hydrogenovibrio from deep sea hydrothermal vents ISME J. (IF 10.8) Pub Date : 2024-09-12 Katja Laufer-Meiser, Malik Alawi, Stefanie Böhnke, Claus-Henning Solterbeck, Jana Schloesser, Axel Schippers, Philipp Dirksen, Thomas Brüser, Susann Henkel, Janina Fuss, Mirjam Perner
Chemolithoautotrophic Hydrogenovibrio are ubiquitous and abundant at hydrothermal vents. They can oxidize sulfur, hydrogen or iron, but none are known to use all three energy sources. This ability though would be advantageous in vents hallmarked by highly dynamic environmental conditions. We isolated three Hydrogenovibrio strains from vents along the Indian Ridge, which grow on all three electron donors
-
Fitness factors impacting survival of a subsurface bacterium in contaminated groundwater ISME J. (IF 10.8) Pub Date : 2024-09-12 Michael P Thorgersen, Jennifer L Goff, Valentine V Trotter, Farris L Poole, Adam P Arkin, Adam M Deutschbauer, Michael W W Adams
Many factors contribute to the ability of a microbial species to persist when encountering complexly contaminated environments including time of exposure, the nature and concentration of contaminants, availability of nutritional resources, and possession of a combination of appropriate molecular mechanisms needed for survival. Herein we sought to identify genes that are most important for survival
-
Protist predation promotes antimicrobial resistance spread through antagonistic microbiome interactions ISME J. (IF 10.8) Pub Date : 2024-09-11 Chen Liu, Yijin Wang, Zeyuan Zhou, Shimei Wang, Zhong Wei, Mohammadhossein Ravanbakhsh, Qirong Shen, Wu Xiong, George A Kowalchuk, Alexandre Jousset
None declared.Conflicts of interestAntibiotic resistance has grown into a major public health threat. In this study, we reveal predation by protists as an overlooked driver of antibiotic resistance dissemination in the soil microbiome. While previous studies have primarily focused on the distribution of antibiotic resistance genes, our work sheds light on the pivotal role of soil protists in shaping
-
Heterotrophic nitrification by Alcaligenes faecalis links organic and inorganic nitrogen metabolism ISME J. (IF 10.8) Pub Date : 2024-09-10 Ya-Ling Qin, Zong-Lin Liang, Guo-Min Ai, Wei-Feng Liu, Yong Tao, Cheng-Ying Jiang, Shuang-Jiang Liu, De-Feng Li
Heterotrophic nitrification remains a mystery for decades. It has been commonly hypothesized that heterotrophic nitrifiers oxidize ammonia to hydroxylamine and then to nitrite in a way similar to autotrophic AOA and AOB. Recently, heterotrophic nitrifiers from Alcaligenes were found to oxidize ammonia to hydroxylamine and then to N2 (“dirammox”, direct ammonia oxidation) by the gene cluster dnfABC
-
Metabolite release by nitrifiers facilitates metabolic interactions in the ocean ISME J. (IF 10.8) Pub Date : 2024-09-08 Barbara Bayer, Shuting Liu, Katherine Louie, Trent R Northen, Michael Wagner, Holger Daims, Craig A Carlson, Alyson E Santoro
Microbial chemoautotroph-heterotroph interactions may play a pivotal role in the cycling of carbon in the deep ocean, reminiscent of phytoplankton-heterotroph associations in surface waters. Nitrifiers are the most abundant chemoautotrophs in the global ocean, yet very little is known about nitrifier metabolite production, release, and transfer to heterotrophic microbial communities. To elucidate which
-
Ammonia leakage can underpin nitrogen-sharing among soil microorganisms ISME J. (IF 10.8) Pub Date : 2024-09-05 Luke Richards, Kelsey Cremin, Mary Coates, Finley Vigor, Patrick Schäfer, Orkun S Soyer
Soil microbial communities host a large number of microbial species that support important ecological functions such as biogeochemical cycling and plant nutrition. The extent and stability of these functions are affected by inter-species interactions among soil microorganisms, yet the different mechanisms underpinning microbial interactions in the soil are not fully understood. Here, we study the extent
-
Interplay between particle size and microbial ecology in the gut microbiome ISME J. (IF 10.8) Pub Date : 2024-08-30 Jeffrey Letourneau, Verónica M Carrion, Jun Zeng, Sharon Jiang, Olivia W Osborne, Zachary C Holmes, Aiden Fox, Piper Epstein, Chin Yee Tan, Michelle Kirtley, Neeraj K Surana, Lawrence A David
Physical particles can serve as critical abiotic factors that structure the ecology of microbial communities. For non-human vertebrate gut microbiomes, fecal particle size (FPS) has been known to be shaped by chewing efficiency and diet. However, little is known about what drives FPS in the human gut. Here, we analyzed FPS by laser diffraction across a total of 76 individuals and found FPS to be strongly
-
Evolutionary history and origins of Dsr-mediated sulfur oxidation ISME J. (IF 10.8) Pub Date : 2024-08-29 Katherine M Klier, Cody Martin, Marguerite V Langwig, Karthik Anantharaman
None declared.Conflicts of interestMicroorganisms play vital roles in sulfur cycling through the oxidation of elemental sulfur and reduction of sulfite. These metabolisms are catalyzed by dissimilatory sulfite reductases (Dsr) functioning in either the reductive or reverse, oxidative direction. Dsr-mediated sulfite reduction is an ancient metabolism proposed to have fueled energy metabolism in some
-
Gut microbiota dysbiosis deteriorates immunoregulatory effects of tryptophan via colonic indole and LBP/HTR2B-mediated macrophage function ISME J. (IF 10.8) Pub Date : 2024-08-24 Lili Jiang, Youling Hao, Dandan Han, Wenjian Dong, Aoyu Yang, Zhiyuan Sun, Yao Ge, Shuai Duan, Xiuwen Zhang, Zhaolai Dai
Tryptophan (Trp) has been shown to regulate immune function by modulating gut serotonin (5-HT) metabolism and signaling. However, the mechanisms underlying the microbial modulation of gut 5-HT signaling in gut inflammation with gut microbiota dysbiosis require further investigation. Here, we investigated the effects of Trp supplementation on the composition and metabolism of the gut microbiome and
-
Adaptation strategies of giant viruses to low-temperature marine ecosystems ISME J. (IF 10.8) Pub Date : 2024-08-23 Marianne Buscaglia, José Luis Iriarte, Frederik Schulz, Beatriz Díez
Microbes in marine ecosystems have evolved their gene content to thrive successfully in the cold. Although this process has been reasonably well studied in bacteria and selected eukaryotes, less is known about the impact of cold environments on the genomes of viruses that infect eukaryotes. Here, we analyzed cold adaptations in giant viruses (Nucleocytoviricota and Mirusviricota) from austral marine
-
Temperature modulates dominance of a superinfecting Arctic virus in its unicellular algal host ISME J. (IF 10.8) Pub Date : 2024-08-22 Claudia Meyer, Victoria L N Jackson, Keith Harrison, Ioanna Fouskari, Henk Bolhuis, Yael A Artzy-Randrup, Jef Huisman, Adam Monier, Corina P D Brussaard
Complex virus-virus interactions can arise when multiple viruses coinfect the same host, impacting infection outcomes with broader ecological and evolutionary significance for viruses and host. Yet, our knowledge regarding virus competition is still limited, especially for single-celled eukaryotic host-virus systems. Here, we report on mutual interference of two dsDNA viruses, MpoV-45 T and MpoV-46
-
Bacterial chemolithoautotrophy in ultramafic plumes along the Mid-Atlantic Ridge. ISME J. (IF 10.8) Pub Date : 2024-01-08 Bledina Dede,Eoghan P Reeves,Maren Walter,Wolfgang Bach,Rudolf Amann,Anke Meyerdierks
Hydrothermal vent systems release reduced chemical compounds that act as an important energy source in the deep sea. Chemolithoautotrophic microbes inhabiting hydrothermal plumes oxidize these compounds, in particular, hydrogen and reduced sulfur, to obtain the energy required for CO2 fixation. Here, we analysed the planktonic communities of four hydrothermal systems located along the Mid-Atlantic
-
Methanogenic symbionts of anaerobic ciliates are host and habitat specific. ISME J. (IF 10.8) Pub Date : 2024-01-08 Daniel Méndez-Sánchez,Anna Schrecengost,Johana Rotterová,Kateřina Koštířová,Roxanne A Beinart,Ivan Čepička
The association between anaerobic ciliates and methanogenic archaea has been recognized for over a century. Nevertheless, knowledge of these associations is limited to a few ciliate species, and so the identification of patterns of host-symbiont specificity has been largely speculative. In this study, we integrated microscopy and genetic identification to survey the methanogenic symbionts of 32 free-living
-
Nitrite-oxidizing bacteria adapted to low oxygen conditions dominate nitrite oxidation in marine oxygen minimum zones ISME J. (IF 10.8) Pub Date : 2024-08-14 Samantha G Fortin, Xin Sun, Amal Jayakumar, Bess B Ward
Nitrite is a central molecule in the nitrogen cycle because nitrite oxidation to nitrate (an aerobic process) retains fixed nitrogen in a system and its reduction to dinitrogen gas (anaerobic) reduces the fixed nitrogen inventory. Despite its acknowledged requirement for oxygen, nitrite oxidation is observed in oxygen-depleted layers of the ocean’s oxygen minimum zones (OMZs), challenging the current
-
Hidden genomic diversity drives niche partitioning in a cosmopolitan eukaryotic picophytoplankton ISME J. (IF 10.8) Pub Date : 2024-08-14 Yangbing Xu, Shara K K Leung, Taylor M W Li, Charmaine C M Yung
Marine eukaryotic phytoplankton are fundamental to the marine food web, yet the lack of reference genomes or just a single genome representing a taxon has led to an underestimation of their taxonomic, adaptive, and functional diversity. Here, we integrated strain isolation with metagenomic binning to recover genomes from the cosmopolitan picophytoplankton genus Bathycoccus, traditionally considered
-
Bacterial growth and environmental adaptation via thiamine biosynthesis and thiamine-mediated metabolic interactions ISME J. (IF 10.8) Pub Date : 2024-08-12 Xihui Xu, Can Li, Weimiao Cao, Lulu Yan, Lulu Cao, Qi Han, Minling Gao, Yahua Chen, Zhenguo Shen, Jiandong Jiang, Chen Chen
Understanding the ancestral transition from anaerobic to aerobic lifestyles is essential for comprehending life’s early evolution. However, the biological adaptations occurring during this crucial transition remain largely unexplored. Thiamine is an important cofactor involved in central carbon metabolism and aerobic respiration. Here, we explored the phylogenetic and global distribution of thiamine-auxotrophic
-
Temperature-dependent trophic associations modulate soil bacterial communities along latitudinal gradients ISME J. (IF 10.8) Pub Date : 2024-08-08 Xing Huang, Jianjun Wang, Kenneth Dumack, Karthik Anantharaman, Bin Ma, Yan He, Weiping Liu, Hongjie Di, Yong Li, Jianming Xu
Understanding the environmental and biological mechanisms shaping latitudinal patterns in microbial diversity is challenging in the field of ecology. Although multiple hypotheses have been proposed to explain these patterns, a consensus has rarely been reached. Here, we conducted a large-scale field survey and microcosm experiments to investigate how environmental heterogeneity and putative trophic
-
Niche separation in bacterial communities and activities in porewater, loosely attached, and firmly attached fractions in permeable surface sediments ISME J. (IF 10.8) Pub Date : 2024-08-08 Chyrene Moncada, Carol Arnosti, Jan D Brüwer, Dirk de Beer, Rudolf Amann, Katrin Knittel
Heterotrophic microbes are central to organic matter degradation and transformation in marine sediments. Currently, most investigations of benthic microbiomes do not differentiate between processes in the porewater and on the grains and, hence, only show a generalized picture of the community. This limits our understanding of the structure and functions of sediment microbiomes. To address this problem
-
Molecular mechanisms and environmental adaptations of flagellar loss and biofilm growth of Rhodanobacter under environmental stress ISME J. (IF 10.8) Pub Date : 2024-08-08 Mingfei Chen, Valentine V Trotter, Peter J Walian, Yan Chen, Romario Lopez, Lauren M Lui, Torben N Nielsen, Ria Gracielle Malana, Michael P Thorgersen, Andrew J Hendrickson, Heloise Carion, Adam M Deutschbauer, Christopher J Petzold, Heidi J Smith, Adam P Arkin, Michael W W Adams, Matthew W Fields, Romy Chakraborty
Biofilms aid bacterial adhesion to surfaces via direct and indirect mechanisms, and formation of biofilms is considered as an important strategy for adaptation and survival in sub-optimal environmental conditions. However, the molecular underpinnings of biofilm formation in subsurface sediment/groundwater ecosystems where microorganisms often experience fluctuations in nutrient input, pH, nitrate or
-
Large attachment organelle mediates interaction between Nanobdellota archaeon YN1 and its host ISME J. (IF 10.8) Pub Date : 2024-08-08 Matthew D Johnson, Hiroyuki D Sakai, Bindusmita Paul, Takuro Nunorura, Somavally Dalvi, Manasi Mudaliyar, Doulin C Shepherd, Michiru Shimizu, Shubha Udupa, Moriya Ohkuma, Norio Kurosawa, Debnath Ghosal
DPANN archaea are an enigmatic superphylum that are difficult to isolate and culture in the laboratory due to their specific culture conditions and apparent ectosymbiotic lifestyle. Here we successfully isolated and cultivated a co-culture system of a novel Nanobdellota archaeon YN1 and its host Sulfurisphaera ohwakuensis YN1HA. We characterised the co-culture system by complementary methods, including
-
Production of structurally diverse sphingolipids by anaerobic marine bacteria in the euxinic Black Sea water column ISME J. (IF 10.8) Pub Date : 2024-08-08 Su Ding, F A Bastiaan von Meijenfeldt, Nicole J Bale, Jaap S Sinninghe Damsté, Laura Villanueva
Microbial lipids, used as taxonomic markers and physiological indicators, have mainly been studied through cultivation. However, this approach is limited due to the scarcity of cultures of environmental microbes, thereby restricting insights into the diversity of lipids and their ecological roles. Addressing this limitation, here we apply metalipidomics combined with metagenomics in the Black Sea,
-
Microbial community composition predicts bacterial production across ocean ecosystems ISME J. (IF 10.8) Pub Date : 2024-08-06 Elizabeth Connors, Avishek Dutta, Rebecca Trinh, Natalia Erazo, Srishti Dasarathy, Hugh Ducklow, J L Weissman, Yi-Chun Yeh, Oscar Schofield, Deborah Steinberg, Jed Fuhrman, Jeff S Bowman
Microbial ecological functions are an emergent property of community composition. For some ecological functions this link is strong enough that community composition can be used to estimate the quantity of an ecological function. Here, we apply random forest regression models to compare the predictive performance of community composition and environmental data for bacterial production (BP). Using data
-
Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates ISME J. (IF 10.8) Pub Date : 2024-08-05 Eva Simon, Ksenia Guseva, Sean Darcy, Lauren Alteio, Petra Pjevac, Hannes Schmidt, Kian Jenab, Christian Ranits, Christina Kaiser
Soils provide essential ecosystem services and represent the most diverse habitat on Earth. It has been suggested that the presence of various physico-chemically heterogenous microhabitats supports the enormous diversity of microbial communities in soil. However, little is known about the relationship between microbial communities and their immediate environment at the micro- to millimetre-scale. In
-
Niche differentiation within bacterial key-taxa in stratified surface waters of the Southern Pacific Gyre ISME J. (IF 10.8) Pub Date : 2024-08-03 Monike Oggerin, Tomeu Viver, Jan Brüwer, Daniela Voß, Marina García-Llorca, Oliver Zielinski, Luis H Orellana, Bernhard M Fuchs
One of the most hostile marine habitats on Earth is the surface of the South Pacific Gyre (SPG), characterized by high solar radiation, extreme nutrient depletion and low productivity. During the SO-245 “UltraPac” cruise through the center of the ultra-oligotrophic SPG, the marine alphaproteobacterial group AEGEAN169 was detected by fluorescence in situ hybridization at relative abundances up to 6%
-
Anaerobic hydrocarbon biodegradation by alkylotrophic methanogens in deep oil reservoirs ISME J. (IF 10.8) Pub Date : 2024-08-01 Cui-Jing Zhang, Zhuo Zhou, Guihong Cha, Ling Li, Lin Fu, Lai-Yan Liu, Lu Yang, Gunter Wegener, Lei Cheng, Meng Li
Methanogenic biodegradation of crude oil is a common process in subsurface biodegraded oil reservoirs. This process was previously assigned to syntrophy of hydrocarbon-degrading bacteria, and methanogenic archaea. Recent studies showed that archaea of the Candidatus Methanoliparum named as alkylotrophic methanogens coupled hydrocarbon degradation and methane production in a single archaeon. To assess
-
Anerobic ammonium oxidation coupled to iron(III) reduction catalyzed by a lithoautotrophic nitrate-reducing iron(II) oxidizing enrichment culture ISME J. (IF 10.8) Pub Date : 2024-07-30 Hong-Bin Zhang, He-Fei Wang, Jia-Bo Liu, Zhen Bi, Ruo-Fei Jin, Tian Tian
The last two decades have seen nitrogen/iron-transforming bacteria at the forefront of new biogeochemical discoveries, such as anaerobic ammonium oxidation coupled to ferric iron reduction (feammox) and lithoautotrophic nitrate-reducing ferrous iron-oxidation (NRFeOx). These emerging findings continue to expand our knowledge of the nitrogen/iron cycle in nature, and also highlight the need to re-understand
-
Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin ISME J. (IF 10.8) Pub Date : 2024-07-30 Dagmar Jirsová, Jeremy G Wideman
Stramenopiles represent a significant proportion of aquatic and terrestrial biota. Most biologists can name a few, but these are limited to the phototrophic (e.g., diatoms and kelp) or parasitic species (e.g., oomycetes, Blastocystis), with free-living heterotrophs largely overlooked. Though our attention is slowly turning towards heterotrophs, we have only a limited understanding of their biology
-
Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay ISME J. (IF 10.8) Pub Date : 2024-07-30 Anna Rasmussen, Christopher A Francis
Transient or recurring blooms of ammonia-oxidizing archaea (AOA) have been reported in several estuarine and coastal environments, including recent observations of AOA blooms in South San Francisco Bay (SFB). Here, we measured nitrification rates, quantified AOA abundance, and analyzed both metagenomic and metatranscriptomic data to examine the dynamics and activity of nitrifying microorganisms over
-
Colonization compatibility with Bacillus altitudinis confers soybean seed rot resistance ISME J. (IF 10.8) Pub Date : 2024-07-29 Ping-Hu Wu, Hao-Xun Chang
The plant microbiome and plant-associated bacteria are known to support plant health, but there are limited studies on seed and seedling microbiome to reveal how seed-associated bacteria may confer disease resistance. In this study, the application of antibiotics on soybean seedlings indicated that seed-associated bacteria were involved in the seed rot resistance against a soil-borne pathogen Calonectria
-
Reversed oxidative TCA (roTCA) for carbon fixation by an Acidimicrobiia strain from a saline lake ISME J. (IF 10.8) Pub Date : 2024-07-27 Lei Gao, Lan Liu, Ai-Ping Lv, Lin Fu, Zheng-Han Lian, Takuro Nunoura, Brian P Hedlund, Qing-Yu Xu, Dildar Wu, Jian Yang, Mukhtiar Ali, Meng-Meng Li, Yong-Hong Liu, André Antunes, Hong-Chen Jiang, Lei Cheng, Jian-Yu Jiao, Wen-Jun Li, Bao-Zhu Fang
Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin–Benson–Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs
-
Core microbiome-associated proteins associated with ulcerative colitis interact with cytokines for synergistic or antagonistic effects on gut bacteria ISME J. (IF 10.8) Pub Date : 2024-07-26 Ting Zhang, Hang Zhong, Lu Lin, Zhiyan Zhang, Kewen Xue, Feixiang He, Yingshu Luo, Panpan Wang, Zhi Zhao, Li Cong, Pengfei Pang, Xiaofeng Li, Hong Shan, Zhixiang Yan
Inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), is associated with a loss or an imbalance of host-microorganism interactions. However, such interactions at protein levels remain largely unknown. Here, we applied a depletion-assisted metaproteomics approach to obtain in-depth host-microbiome association networks of IBD, where the core host proteins shifted
-
Scarcity of fixed carbon transfer in a model microbial phototroph-heterotroph interaction ISME J. (IF 10.8) Pub Date : 2024-07-25 Sunnyjoy Dupuis, Usha F Lingappa, Xavier Mayali, Eve S Sindermann, Jordan L Chastain, Peter K Weber, Rhona Stuart, Sabeeha S Merchant
Although the green alga Chlamydomonas reinhardtii has long served as a reference organism, few studies have interrogated its role as a primary producer in microbial interactions. Here, we quantitatively investigated C. reinhardtii’s capacity to support a heterotrophic microbe using the established coculture system with Mesorhizobium japonicum, a vitamin B12-producing α-proteobacterium. Using stable
-
Four years of climate warming reduced dark carbon fixation in coastal wetlands ISME J. (IF 10.8) Pub Date : 2024-07-25 Bolin Liu, Lin Qi, Yanling Zheng, Chao Zhang, Jie Zhou, Zhirui An, Bin Wang, Zhuke Lin, Cheng Yao, Yixuan Wang, Guoyu Yin, Hongpo Dong, Xiaofei Li, Xia Liang, Ping Han, Min Liu, Guosen Zhang, Ying Cui, Lijun Hou
Dark carbon fixation (DCF), conducted mainly by chemoautotrophs, contributes greatly to primary production and the global carbon budget. Understanding the response of DCF process to climate warming in coastal wetlands is of great significance for model optimization and climate change prediction. Here, based on a four-year field warming experiment (average annual temperature increase of 1.5°C), DCF
-
Divergent molecular strategies drive evolutionary adaptation to competitive fitness in biofilm formation ISME J. (IF 10.8) Pub Date : 2024-07-25 Mingxing Tang, Ruixue Yang, Zilin Zhuang, Shuhong Han, Yunke Sun, Peiyu Li, Kewei Fan, Zhao Cai, Qiong Yang, Zhijian Yu, Liang Yang, Shuo Li
Biofilm is a group of heterogeneously structured and densely packed bacteria with limited access to nutrients and oxygen. These intrinsic features can allow a mono-species biofilm to diversify into polymorphic subpopulations, determining the overall community’s adaptive capability to changing ecological niches. However, the specific biological functions underlying biofilm diversification and fitness
-
Chlamydiae as symbionts of photosynthetic dinoflagellates ISME J. (IF 10.8) Pub Date : 2024-07-23 Justin Maire, Astrid Collingro, Kshitij Tandon, Vanta J Jameson, Louise M Judd, Matthias Horn, Linda L Blackall, Madeleine J H van Oppen
Chlamydiae are ubiquitous intracellular bacteria and infect a wide diversity of eukaryotes, including mammals. However, chlamydiae have never been reported to infect photosynthetic organisms. Here, we describe a novel chlamydial genus and species, Candidatus Algichlamydia australiensis, capable of infecting the photosynthetic dinoflagellate Cladocopium sp. (originally isolated from a scleractinian
-
Osmoregulation in freshwater anaerobic methane oxidizing archaea under salt stress ISME J. (IF 10.8) Pub Date : 2024-07-20 Maider J Echeveste Medrano, Andy O Leu, Martin Pabst, Yuemei Lin, Simon J Mcllroy, Gene W Tyson, Jitske van Ede, Irene Sánchez-Andrea, Mike S M Jetten, Robert Jansen, Cornelia U Welte
Climate change-driven sea level rise threatens freshwater ecosystems and elicits salinity stress in microbiomes. Methane emissions in these systems are largely mitigated by methane-oxidizing microorganisms. Here, we characterized the physiological and metabolic response of freshwater methanotrophic archaea to salt stress. In our microcosm experiments, inhibition of methanotrophic archaea started at
-
Housefly gut microbiomes as a reservoir and facilitator for the spread of antibiotic resistance ISME J. (IF 10.8) Pub Date : 2024-07-18 Dehao Gan, Zhenyan Lin, Lingshuang Zeng, Hui Deng, Timothy R Walsh, Shungui Zhou, Qiu E Yang
Arthropods, such as houseflies, play a significant role on the dissemination of antimicrobial resistance (AMR); however, their impact has often been overlooked in comparison to other AMR vectors. Understanding the contribution of arthropods to the spread of AMR is critical for implementing robust policies to mitigate the spread of AMR across “One Health” sectors. Herein, we investigated the in-situ
-
Globally distributed bacteriophage genomes reveal mechanisms of tripartite phage-bacteria-coral interactions ISME J. (IF 10.8) Pub Date : 2024-07-18 Bailey A Wallace, Natascha S Varona, Poppy J Hesketh-Best, Alexandra K Stiffler, Cynthia B Silveira
Reef-building corals depend on an intricate community of microorganisms for functioning and resilience. The infection of coral-associated bacteria by bacteriophages can modify bacteria-host interactions, yet very little is known about phage functions in the holobiont. This gap stems from methodological limitations that have prevented the recovery of high-quality viral genomes and bacterial host assignment
-
Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome ISME J. (IF 10.8) Pub Date : 2024-07-17 Adrián López-Beltrán, João Botelho, Jaime Iranzo
Arms races between mobile genetic elements and prokaryotic hosts are major drivers of ecological and evolutionary change in microbial communities. Prokaryotic defense systems such as CRISPR-Cas have the potential to regulate microbiome composition by modifying the interactions among bacteria, plasmids, and phages. Here, we used longitudinal metagenomic data from 130 healthy and diseased individuals
-
Molecular basis of phenotypic plasticity in a marine ciliate ISME J. (IF 10.8) Pub Date : 2024-07-17 Jiao Pan, Yaohai Wang, Chao Li, Simo Zhang, Zhiqiang Ye, Jiahao Ni, Haichao Li, Yichen Li, Hongwei Yue, Chenchen Ruan, Dange Zhao, Yujian Jiang, Xiaolin Wu, Xiaopeng Shen, Rebecca A Zufall, Yu Zhang, Weiyi Li, Michael Lynch, Hongan Long
Phenotypic plasticity, which involves phenotypic transformation in the absence of genetic change, may serve as a strategy for organisms to survive in complex and highly-fluctuating environments. However, its reaction norm, molecular basis, and evolution remain unclear in most organisms, especially microbial eukaryotes. In this study, we explored these questions by investigating the reaction norm, regulation
-
Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution ISME J. (IF 10.8) Pub Date : 2024-07-12 Tom A Williams, Adrian A Davin, Lénárd L Szánthó, Alexandros Stamatakis, Noah A Wahl, Ben J Woodcroft, Rochelle M Soo, Laura Eme, Paul O Sheridan, Cecile Gubry-Rangin, Anja Spang, Philip Hugenholtz, Gergely J Szöllősi
In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree, and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying
-
Distinctive chemotactic responses of three marine herbivore protists to DMSP and related compounds ISME J. (IF 10.8) Pub Date : 2024-07-11 Queralt Güell-Bujons, Medea Zanoli, Idan Tuval, Albert Calbet, Rafel Simó
Marine planktonic predator–prey interactions occur in microscale seascapes, where diffusing chemicals may act either as chemotactic cues that enhance or arrest predation, or as elemental resources that are complementary to prey ingestion. The phytoplankton osmolyte dimethylsulfoniopropionate (DMSP) and its degradation products dimethylsulfide (DMS) and acrylate are pervasive compounds with high chemotactic
-
Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability ISME J. (IF 10.8) Pub Date : 2024-07-11 Yanfeng Zhao, Alina Bitzer, Jeffrey John Power, Darya Belikova, Benjamin Orlando Torres Salazar, Lea Antje Adolf, David Leon Gerlach, Bernhard Krismer, Simon Heilbronner
The human microbiome is critically associated with human health and disease. One aspect of this is that antibiotic-resistant opportunistic bacterial pathogens such as methicillin-resistant Staphylococcus aureus can reside within the nasal microbiota which increases the risk of infections. Epidemiological studies of the nasal microbiome have revealed positive and negative correlations between non-pathogenic
-
Agricultural intensification reduces selection of putative plant growth-promoting rhizobacteria in wheat ISME J. (IF 10.8) Pub Date : 2024-07-11 Tessa E Reid, Vanessa N Kavamura, Adriana Torres-Ballesteros, Monique E Smith, Maïder Abadie, Mark Pawlett, Ian M Clark, Jim A Harris, Tim H Mauchline
The complex evolutionary history of wheat has shaped its associated root microbial community. However, consideration of impacts from agricultural intensification have been limited. This study investigated how endogenous (genome polyploidization), and exogenous (introduction of chemical fertilizers) factors have shaped beneficial rhizobacterial selection. We combined culture -independent and -dependent
-
Proteomes of native and non-native symbionts reveal responses underpinning host-symbiont specificity in the cnidarian–dinoflagellate symbiosis ISME J. (IF 10.8) Pub Date : 2024-07-11 Amirhossein Gheitanchi Mashini, Clinton A Oakley, Lifeng Peng, Arthur R Grossman, Virginia M Weis, Simon K Davy
Cellular mechanisms responsible for the regulation of nutrient exchange, immune responses, and symbiont population growth in the cnidarian-dinoflagellate symbiosis are poorly resolved, particularly with respect to the dinoflagellate symbiont. Here, we characterised proteomic changes in the native symbiont Breviolum minutum during colonisation of its host sea anemone Exaiptasia diaphana (“Aiptasia”)
-
Linking active rectal mucosa-attached microbiota to host immunity reveals its role in host-pathogenic STEC O157 interactions ISME J. (IF 10.8) Pub Date : 2024-07-10 Zhe Pan, Yanhong Chen, Mi Zhou, Tim A McAllister, Tom N Mcneilly, Le Luo Guan
The rectal anal junction (RAJ) is the major colonization site of Shiga toxin-producing Escherichia coli (STEC) O157 in beef cattle, leading to transmission of this foodborne pathogen from farms to food chains. To date, there is limited understanding on whether mucosa-attached microbiome has a profound impact on host-STEC interactions. In this study, the active RAJ mucosa-attached microbiota and its
-
Defined synthetic microbial communities colonize and benefit field-grown sorghum ISME J. (IF 10.8) Pub Date : 2024-07-10 Citlali Fonseca-García, Dean Pettinga, Andrew Wilson, Joshua R Elmore, Ryan McClure, Jackie Atim, Julie Pedraza, Robert Hutmacher, Halbay Turumtay, Yang Tian, Aymerick Eudes, Henrik V Scheller, Robert Egbert, Devin Coleman-Derr
The rhizosphere constitutes a dynamic interface between plant hosts and their associated microbial communities. Despite the acknowledged potential for enhancing plant fitness by manipulating the rhizosphere, the engineering of the rhizosphere microbiome through inoculation has posed significant challenges. These challenges are thought to arise from the competitive microbial ecosystem where introduced
-
Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles ISME J. (IF 10.8) Pub Date : 2024-07-08 Yohei Nishikawa, Ryota Wagatsuma, Yuko Tsukada, Lin Chia-ling, Rieka Chijiiwa, Masahito Hosokawa, Haruko Takeyama
Environmental viruses (primarily bacteriophages) are widely recognized as playing an important role in ecosystem homeostasis through the infection of host cells. However, the majority of environmental viruses are still unknown as their mosaic structure and frequent mutations in their sequences hinder genome construction in current metagenomics. To enable the large-scale acquisition of environmental
-
Divergent marine anaerobic ciliates harbor closely related Methanocorpusculum endosymbionts ISME J. (IF 10.8) Pub Date : 2024-07-06 Anna Schrecengost, Johana Rotterová, Kateřina Poláková, Ivan Čepička, Roxanne A Beinart
Ciliates are a diverse group of protists known for their ability to establish various partnerships and thrive in a wide variety of oxygen-depleted environments. Most anaerobic ciliates harbor methanogens, one of the few known archaea living intracellularly. These methanogens increase the metabolic efficiency of host fermentation via syntrophic use of host end-product in methanogenesis. Despite the
-
Geographic population structure and distinct intra-population dynamics of globally abundant freshwater bacteria ISME J. (IF 10.8) Pub Date : 2024-07-03 Matthias Hoetzinger, Martin W Hahn, Linnéa Y Andersson, Nathaniel Buckley, Chelsea Ramsin, Moritz Buck, Julia K Nuy, Sarahi L Garcia, Fernando Puente-Sánchez, Stefan Bertilsson
Implications of geographic separation and temporal dynamics on the evolution of free-living bacterial species are widely unclear. However, the vast amount of metagenome sequencing data generated during the last decades from various habitats around the world provides an unprecedented opportunity for such investigations. Here we exploited publicly available and new freshwater metagenomes in combination
-
Type IV secretion system effector sabotages multiple defense systems in a competing bacterium ISME J. (IF 10.8) Pub Date : 2024-07-03 Bingxin Wang, Fugui Xu, Zeyu Zhang, Danyu Shen, Limin Wang, Huijun Wu, Qing Yan, Chuanbin Cui, Pingping Wang, Qi Wei, Xiaolong Shao, Mengcen Wang, Guoliang Qian
Effector proteins secreted by bacteria that infect mammalian and plant cells often subdue eukaryotic host cell defenses by simultaneously affecting multiple targets. However, instances when a bacterial effector injected in the competing bacteria sabotage more than a single target have not been reported. Here, we demonstrate that the effector protein, LtaE, translocated by the type IV secretion system
-
Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health ISME J. (IF 10.8) Pub Date : 2024-07-02 Sang-Moo Lee, Roniya Thapa Magar, Min Kyeong Jung, Hyun Gi Kong, Ju Yeon Song, Joo Hwan Kwon, Minseo Choi, Hyoung Ju Lee, Seung Yeup Lee, Raees Khan, Jihyun F Kim, Seon-Woo Lee
Microbial interactions impact the functioning of microbial communities. However, microbial interactions within host-associated communities remains poorly understood. Here, we report that the beneficiary rhizobacterium Niallia sp. RD1 requires the helper Pseudomonas putida H3 for bacterial growth and beneficial interactions with the plant host. In the absence of the helper H3 strain, the Niallia sp
-
Cellular interactions and evolutionary origins of endosymbiotic relationships with ciliates ISME J. (IF 10.8) Pub Date : 2024-06-25 Qi Song, Fangqing Zhao, Lina Hou, Miao Miao
As unicellular predators, ciliates engage in close associations with diverse microbes, laying the foundation for the establishment of endosymbiosis. Originally heterotrophic, ciliates demonstrate the ability to acquire phototrophy by phagocytizing unicellular algae or by sequestering algal plastids. This adaptation enables them to gain photosynthate and develop resistance to unfavorable environmental
-
Interspecies ecological competition rejuvenates decayed Geobacter electroactive biofilm ISME J. (IF 10.8) Pub Date : 2024-06-25 Yin Ye, Lu Zhang, Xiaohui Hong, Man Chen, Xing Liu, Shungui Zhou
Bioelectrochemical systems (BESs) exploit electroactive biofilms (EABs) for promising applications in biosensing, wastewater treatment, energy production and chemical biosynthesis. However, during the operation of BESs, EABs inevitably decay. Seeking approaches to rejuvenate decayed EABs is critical for the sustainability and practical application of BESs. Prophage induction has been recognized as
-
Chemolithoautotrophic diazotrophs dominate dark nitrogen fixation in mangrove sediments ISME J. (IF 10.8) Pub Date : 2024-06-25 Shasha Wang, Lijing Jiang, Zhuoming Zhao, Zhen Chen, Jun Wang, Karine Alain, Liang Cui, Yangsheng Zhong, Yongyi Peng, Qiliang Lai, Xiyang Dong, Zongze Shao
Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. So far chemolithoautotrophic bacteria are widely recognized as the principal diazotrophs in oligotrophic marine and terrestrial ecosystems. However, the contribution of chemolithoautotrophs to nitrogen fixation in organic-rich habitats remains unclear. Here, we utilized metagenomic and metatranscriptomic approaches
-
Aerobic denitrification as an N2O source from microbial communities ISME J. (IF 10.8) Pub Date : 2024-06-24 Nina Roothans, Minke Gabriëls, Thomas Abeel, Martin Pabst, Mark C M van Loosdrecht, Michele Laureni
Nitrous oxide (N2O) is a potent greenhouse gas of primarily microbial origin. Oxic and anoxic emissions are commonly ascribed to autotrophic nitrification and heterotrophic denitrification, respectively. Beyond this established dichotomy, we quantitatively show that heterotrophic denitrification can significantly contribute to aerobic nitrogen turnover and N2O emissions in complex microbiomes exposed