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Spatial sensing as a strategy for public goods regulation by gut microbes. ISME J. (IF 10.8) Pub Date : 2024-11-26 I Hashem,A Zhang,J Van Impe
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Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains ISME J. (IF 10.8) Pub Date : 2024-11-23 María Dolores Ramos-Barbero, Borja Aldeguer-Riquelme, Tomeu Viver, Judith Villamor, Miryam Carrillo-Bautista, Cristina López-Pascual, Konstantinos T Konstantinidis, Manuel Martínez-García, Fernando Santos, Ramon Rossello-Mora, Josefa Antón
Viruses shape microbial community structure and activity through the control of population diversity and cell abundances. Identifying and monitoring the dynamics of specific virus-host pairs in nature is hampered by the limitations of culture-independent approaches such as metagenomics, which do not always provide strain-level resolution, and culture-based analyses, which eliminate the ecological background
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Trophic modulation of endophytes by rhizosphere protists ISME J. (IF 10.8) Pub Date : 2024-11-20 Rasit Asiloglu, Seda Ozer Bodur, Solomon Oloruntoba Samuel, Murat Aycan, Jun Murase, Naoki Harada
The plant-microbe interactions, which is crucial for plant health and productivity, mainly occur in rhizosphere: a narrow zone of soil surrounding roots of living plants. The rhizosphere hosts one of the most intense habitats for microbial prey–predator interactions, especially between predatory protists and bacteria. Here, based on two key facts, microbial predators modulate rhizobacterial community
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Coastal bacteria and protists assimilate viral carbon and nitrogen ISME J. (IF 10.8) Pub Date : 2024-11-13 Joaquín Martínez Martínez, David Talmy, Jeffrey A Kimbrel, Peter K Weber, Xavier Mayali
Free viruses are the most abundant type of biological particles in the biosphere, but the lack of quantitative knowledge about their consumption by heterotrophic protists and bacterial degradation has hindered the inclusion of virovory in biogeochemical models. Using isotope-labeled viruses added to three independent microcosm experiments with natural microbial communities followed by isotope measurements
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Pathobiont and symbiont contribute to microbiota homeostasis through Malpighian tubules-gut countercurrent flow in Bactrocera dorsalis ISME J. (IF 10.8) Pub Date : 2024-11-12 Yanning Liu, Rengang Luo, Shuai Bai, Bruno Lemaitre, Hongyu Zhang, Xiaoxue Li
Host-gut microbiota interactions are more complex than good or bad. Both gut symbiotic bacteria and pathobionts can provide essential functions to their host in one scenario and yet be detrimental to host health in another. So, these gut-dwelling bacteria must be tightly controlled to avoid harmful effects on the host. However, how pathobionts and other symbiotic bacteria coordinate to establish a
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Urea assimilation and oxidation support activity of phylogenetically diverse microbial communities of the dark ocean ISME J. (IF 10.8) Pub Date : 2024-11-11 Nestor Arandia-Gorostidi, Alexander L Jaffe, Alma E Parada, Bennett J Kapili, Karen L Casciotti, Rebecca S R Salcedo, Chloé M J Baumas, Anne E Dekas
Urea is hypothesized to be an important source of nitrogen and chemical energy to microorganisms in the deep sea; however, direct evidence for urea use below the epipelagic ocean is lacking. Here, we explore urea utilization from 50 to 4000 meters depth in the northeastern Pacific Ocean using metagenomics, nitrification rates, and single-cell stable-isotope-uptake measurements with nanoscale secondary
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Isolate-anchored comparisons reveal evolutionary and functional differentiation across SAR86 marine bacteria ISME J. (IF 10.8) Pub Date : 2024-11-09 Oscar Ramfelt, Kelle C Freel, Sarah J Tucker, Olivia D Nigro, Michael S Rappé
SAR86 is one of the most abundant groups of bacteria in the global surface ocean. However, since its discovery over 30 years ago, it has remained recalcitrant to isolation and many details regarding this group are still unknown. Here we report the cellular characteristics from the first SAR86 isolate brought into culture, Magnimaribacter mokuoloeensis strain HIMB1674, and use its closed genome in concert
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Microbiome science of human excrement composting ISME J. (IF 10.8) Pub Date : 2024-11-09 Jeff Meilander, J Gregory Caporaso
Linear waste management systems are unsustainable and contribute to environmental degradation, economic inequity, and health disparities. Among the array of environmental challenges stemming from anthropogenic impacts, the management of human excrement (human feces and urine) stands as a significant concern. Over two billion people do not have access to adequate sanitation, signifying a global public
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Aminolipids in bacterial membranes and the natural environment ISME J. (IF 10.8) Pub Date : 2024-11-09 Shengwei Liu, Eleonora Silvano, Mingyu Li, Michaela Mausz, Branko Rihtman, Richard Guillonneau, Otto Geiger, David J Scanlan, Yin Chen
Our comprehension of membrane function has predominantly advanced through research on glycerophospholipids, also known as phosphoglycerides, which are glycerol phosphate-based lipids found across all three domains of life. However, in bacteria, a perplexing group of lipids distinct from glycerol phosphate-based ones also exists. These are amino acid-containing lipids that form an amide bond between
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Biotics and bacterial function: impact on gut and host health ISME J. (IF 10.8) Pub Date : 2024-11-05 Anwar Kandari, Ma’en Al-Odat, Fawaz Alzaid, Karen P Scott
The human gut microbiota, the vast community of microbes inhabiting the gastrointestinal tract, plays a pivotal role in maintaining health. Bacteria are the most abundant organism, and the composition of bacterial communities is strongly influenced by diet. Gut bacteria can degrade complex dietary carbohydrates to produce bioactive compounds such as short-chain fatty acids. Such products influence
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Sheaths are diverse and abundant cell surface layers in archaea ISME J. (IF 10.8) Pub Date : 2024-11-05 Sofia Medvedeva, Guillaume Borrel, Simonetta Gribaldo
Prokaryotic cells employ multiple protective layers crucial for defense, structural integrity, and cellular interactions in the environment. Archaea often feature an S-layer, with some species possessing additional and remarkably resistant sheaths. The archaeal sheath has been studied in Methanothrix and Methanospirillum, revealing a complex structure consisting of amyloid proteins organized into rings
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Genome-resolved metaproteogenomic and nanosolid characterization of an inactive vent chimney densely colonized by enigmatic DPANN archaea ISME J. (IF 10.8) Pub Date : 2024-11-05 Hinako Takamiya, Mariko Kouduka, Shingo Kato, Hiroki Suga, Masaki Oura, Tadashi Yokoyama, Michio Suzuki, Masaru Mori, Akio Kanai, Yohey Suzuki
Recent successes in the cultivation of DPANN archaea with their hosts have demonstrated an episymbiotic lifestyle, whereas the lifestyle of DPANN archaea in natural habitats is largely unknown. A free-living lifestyle is speculated in oxygen-deprived fluids circulated through rock media, where apparent hosts of DPANN archaea are lacking. Alternatively, DPANN archaea may be detached from their hosts
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Impact of timing on the invasion of synthetic bacterial communities ISME J. (IF 10.8) Pub Date : 2024-11-05 Keven D Dooley, Lucas P Henry, Joy Bergelson
Microbial communities regularly experience ecological invasions that can lead to changes in composition and function. Factors thought to impact susceptibility to invasions, such as diversity and resource use, vary over the course of community assembly. We used synthetic bacterial communities to evaluate the success and impact of invasions occurring at different times during the community assembly process
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Bacterial population-level trade-offs between drought tolerance and resource acquisition traits impact decomposition ISME J. (IF 10.8) Pub Date : 2024-11-04 Ashish A Malik, Jennifer B H Martiny, Antonio Ribeiro, Paul O Sheridan, Claudia Weihe, Eoin L Brodie, Steven D Allison
Microbes drive fundamental ecosystem processes such as decomposition. Environmental stressors are known to affect microbes, their fitness, and the ecosystem functions that they perform, yet understanding the causal mechanisms behind this influence has been difficult. We used leaf litter on soil surface as a model in situ system to assess changes in bacterial genomic traits and decomposition rates over
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Probiotic model for studying rhizosphere interactions of root exudates and the functional microbiome ISME J. (IF 10.8) Pub Date : 2024-11-04 Zhiqiang Pang, Peng Xu
Root exudates are important mediators of plant–microbiome interactions. Recent pioneering studies on various aerial root plants, including cereals, have shown that carbohydrate-rich mucilage can enrich diazotrophs and increase host nitrogen utilization and growth. Moreover, non-diazotrophic "gatekeeper" microorganisms in mucilage help defend against pathogenic and environmental microbes. These findings
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Saccharomyces boulardii enhances anti-inflammatory effectors and AhR activation via metabolic interactions in probiotic communities ISME J. (IF 10.8) Pub Date : 2024-11-03 Karl Alex Hedin, Mohammad H Mirhakkak, Troels Holger Vaaben, Carmen Sands, Mikael Pedersen, Adam Baker, Ruben Vazquez-Uribe, Sascha Schäuble, Gianni Panagiotou, Anja Wellejus, Morten Otto Alexander Sommer
Metabolic exchanges between strains in gut microbial communities shape their composition and interactions with the host. This study investigates the metabolic synergy between potential probiotic bacteria and Saccharomyces boulardii, aiming to enhance anti-inflammatory effects within a multi-species probiotic community. By screening a collection of 85 potential probiotic bacterial strains, we identified
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Cyanorhodopsin-II represents a yellow-absorbing proton-pumping rhodopsin clade within cyanobacteria ISME J. (IF 10.8) Pub Date : 2024-11-01 Masumi Hasegawa-Takano, Toshiaki Hosaka, Keiichi Kojima, Yosuke Nishimura, Marie Kurihara, Yu Nakajima, Yoshiko Ishizuka-Katsura, Tomomi Kimura-Someya, Mikako Shirouzu, Yuki Sudo, Susumu Yoshizawa
Microbial rhodopsins are prevalent in many cyanobacterial groups as a light-energy-harvesting system in addition to the photosynthetic system. It has been suggested that this dual system allows efficient capture of sunlight energy using complementary ranges of absorption wavelengths. However, the diversity of cyanobacterial rhodopsins, particularly in accumulated metagenomic data, remains underexplored
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Chronic exposure to polycyclic aromatic hydrocarbons alters skin virome composition and virus–host interactions ISME J. (IF 10.8) Pub Date : 2024-10-25 Shicong Du, Xinzhao Tong, Marcus H Y Leung, Richard J Betts, Anthony C Woo, Philippe Bastien, Namita Misra, Luc Aguilar, Cécile Clavaud, Patrick K H Lee
Exposure to polycyclic aromatic hydrocarbons (PAHs) in polluted air influences the composition of the skin microbiome, which in turn is associated with altered skin phenotypes. However, the interactions between PAH exposure and viromes are unclear. This study aims to elucidate how PAH exposure affects the composition and function of skin viruses, their role in shaping the metabolism of bacterial hosts
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Marine N2-fixer Crocosphaera waterburyi ISME J. (IF 10.8) Pub Date : 2024-10-23 Catie S Cleveland, Kendra A Turk-Kubo, Yiming Zhao, Jonathan P Zehr, Eric A Webb
Marine N2-fixing cyanobacteria, including the unicellular genus Crocosphaera, are considered keystone species in marine food webs. Crocosphaera are globally distributed and provide new sources of nitrogen and carbon, which fuel oligotrophic microbial communities and upper trophic levels. Despite their ecosystem importance, only one pelagic, oligotrophic, phycoerythrin-rich species, Crocosphaera watsonii
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Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles ISME J. (IF 10.8) Pub Date : 2024-10-23 Siddharth Uppal, Samantha C Waterworth, Alina Nick, Heiko Vogel, Laura V Flórez, Martin Kaltenpoth, Jason C Kwan
Microbial symbionts associate with multicellular organisms on a continuum from facultative associations to mutual codependency. In the oldest intracellular symbioses there is exclusive vertical symbiont transmission, and co-diversification of symbiotic partners over millions of years. Such symbionts often undergo genome reduction due to low effective population sizes, frequent population bottlenecks
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Metagenomic time-series reveals a western English Channel viral community dominated by members with strong seasonal signals ISME J. (IF 10.8) Pub Date : 2024-10-23 Luis M Bolaños, Michelle Michelsen, Ben Temperton
Marine viruses are key players of ocean biogeochemistry, profoundly influencing microbial community ecology and evolution. Despite their importance, few studies have explored continuous inter-seasonal viral metagenomic time-series in marine environments. Viral dynamics are complex, influenced by multiple factors such as host population dynamics and environmental conditions. To disentangle the complexity
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Trade-offs between receptor modification and fitness drive host-bacteriophage co-evolution leading to phage extinction or co-existence ISME J. (IF 10.8) Pub Date : 2024-10-23 Lin Chen, Xue Zhao, Shelyn Wongso, Zhuohui Lin, Siyun Wang
Parasite–host co-evolution results in population extinction or co-existence, yet the factors driving these distinct outcomes remain elusive. In this study, Salmonella strains were individually co-evolved with the lytic phage SF1 for 30 days, resulting in phage extinction or co-existence. We conducted a systematic investigation into the phenotypic and genetic dynamics of evolved host cells and phages
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Taeniasis impacts human gut microbiome composition and function ISME J. (IF 10.8) Pub Date : 2024-10-23 Wenjie Mu, Pingping Ma, Yugui Wang, Yaqi Li, Yingying Ding, Yang Zou, Lixia Pu, Qi Yan, Haoyue Kong, Xiaola Guo, Aijiang Guo, Hailong Li, Shuai Wang
Human taeniasis, caused by Taenia tapeworms, is a global parasitic disease with significant implications for public health and food safety. These tapeworms can grow to considerable sizes and potentially impact the microecology of the host gut. Despite their importance, the effects of Taenia infection on host gut microbiota haven’t been thoroughly investigated. In this study, we conducted a cross-sectional
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Ecological success of extreme halophiles subjected to recurrent osmotic disturbances is primarily driven by congeneric species replacement ISME J. (IF 10.8) Pub Date : 2024-10-23 Esteban Bustos-Caparros, Tomeu Viver, Juan F Gago, Luis Miguel Rodriguez-Rojas, Janet K Hatt, Stephanus N Venter, Bernhard M Fuchs, Rudolf Amann, Rafael Bosch, Konstantinos T Konstantinidis, Ramon Rossello-Mora
To understand how extreme halophiles respond to recurrent disturbances, we challenged the communities thriving in salt-saturated (~36% salts) ~230 L brine mesocosms to repeated dilutions down to 13% (D13 mesocosm) or 20% (D20 mesocosm) salts each time mesocosms reached salt saturation due to evaporation (for 10 and 17 cycles, respectively) over 813 days. Depending on the magnitude of dilution, the
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Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health ISME J. (IF 10.8) Pub Date : 2024-10-22 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
None declared.Conflicts of interestMicrobial 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
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Prophages in Vibrio ISME J. (IF 10.8) Pub Date : 2024-10-17 Kerrin Steensen, Joana Séneca, Nina Bartlau, Xiaoqian A Yu, Fatima A Hussain, Martin F Polz
Although tailed bacteriophages (phages) of the class Caudoviricetes are thought to constitute the most abundant and ecologically relevant group of phages that can integrate their genome into the host chromosome, it is becoming increasingly clear that other prophages are widespread. Here, we show that prophages derived from filamentous and tailless phages with genome sizes below 16 kb make up the majority
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Resource sharing of an infant gut microbiota synthetic community in combinations of human milk oligosaccharides ISME J. (IF 10.8) Pub Date : 2024-10-17 Athanasia Ioannou, Maryse D Berkhout, William T Scott, Bernadet Blijenberg, Sjef Boeren, Marko Mank, Jan Knol, Clara Belzer
Quickly after birth, the gut microbiota is shaped via species acquisition and resource pressure. Breastmilk, and more specifically, human milk oligosaccharides are a determining factor in the formation of microbial communities and the interactions between bacteria. Prominent human milk oligosaccharide degraders have been rigorously characterized, but it is not known how the gut microbiota is shaped
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Algae-fungi symbioses and bacteria-fungi co-exclusion drive tree species-specific differences in canopy bark microbiomes ISME J. (IF 10.8) Pub Date : 2024-10-17 Jule Freudenthal, Kenneth Dumack, Stefan Schaffer, Martin Schlegel, Michael Bonkowski
With over 3 trillion trees, forest ecosystems comprise nearly one-third of the terrestrial surface of the Earth. Very little attention has been given to the exploration of the above-ground plant microbiome of trees, its complex trophic interactions, and variations among tree species. To address this knowledge gap, we applied a primer-independent shotgun metatranscriptomic approach to assess the entire
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Nitrate-dependent antimony oxidase in an uncultured Symbiobacteriaceae member ISME J. (IF 10.8) Pub Date : 2024-10-16 Liying Wang, Zhipeng Yin, Wei Yan, Jialong Hao, Fei Tian, Jianbo Shi
Autotrophic antimony (Sb) oxidation coupled to nitrate reduction plays an important role in the transformation and detoxification of Sb. However, the specific oxidase involved in this process has yet to be identified. Herein, we enriched the microbiota capable of nitrate-dependent Sb(III) oxidation and identified a new Sb(III) oxidase in an uncultured member of Symbiobacteriaceae. Incubation experiments
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Activity of novel virus families infecting soil nitrifiers is concomitant with host niche differentiation ISME J. (IF 10.8) Pub Date : 2024-10-16 Sungeun Lee, Christina Hazard, Graeme W Nicol
Chemolithoautotrophic nitrifiers are model groups for linking phylogeny, evolution, and ecophysiology. Ammonia-oxidising bacteria (AOB) typically dominate the first step of ammonia oxidation at high ammonium supply rates, ammonia-oxidising archaea (AOA) and complete ammonia-oxidising Nitrospira (comammox) are often active at lower supply rates or during AOB inactivity, and nitrite-oxidising bacteria
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Gut microbiota carbon and sulfur metabolisms support Salmonella infections ISME J. (IF 10.8) Pub Date : 2024-10-15 Ikaia Leleiwi, Katherine Kokkinias, Yongseok Kim, Maryam Baniasad, Michael Shaffer, Anice Sabag-Daigle, Rebecca A Daly, Rory M Flynn, Vicki H Wysocki, Brian M M Ahmer, Mikayla A Borton, Kelly C Wrighton
Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome
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Dispersal of microbes from grassland fire smoke to soils ISME J. (IF 10.8) Pub Date : 2024-10-15 Adam J Ellington, Kendra Walters, Brent C Christner, Sam Fox, Krista Bonfantine, Cassie Walker, Phinehas Lampman, David C Vuono, Michael Strickland, Katie Lambert, Leda N Kobziar
Wildland fire is increasingly recognized as a driver of bioaerosol emissions, but the effects that smoke-emitted microbes have on the diversity and community assembly patterns of the habitats where they are deposited remain unknown. In this study, we examined whether microbes aerosolized by biomass burning smoke detectably impact the composition and function of soil sinks using lab-based mesocosm experiments
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Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods ISME J. (IF 10.8) Pub Date : 2024-10-12 Tobyn Branck, Zhiji Hu, William A Nickols, Aaron M Walsh, Amrisha Bhosle, Meghan I Short, Jacob T Nearing, Francesco Asnicar, Lauren J McIver, Sagun Maharjan, Ali Rahnavard, Artemis Louyakis, Dayakar V Badri, Christoph Brockel, Kelsey N Thompson, Curtis Huttenhower
The gut microbiome of companion animals is relatively underexplored, despite its relevance to animal health, pet owner health, and basic microbial community biology. Here, we provide the most comprehensive analysis of the canine and feline gut microbiomes to date, incorporating 2639 stool shotgun metagenomes (2272 dog and 367 cat) spanning 14 publicly available datasets (n = 730) and 8 new study populations
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Sulfur-oxidizing symbionts colonize the digestive tract of their Lucinid hosts ISME J. (IF 10.8) Pub Date : 2024-10-10 Cristina M Alcaraz, Joana Séneca, Martin Kunert, Christopher Pree, Marta Sudo, Jillian M Petersen
Like many marine invertebrates, marine lucinid clams have an intimate relationship with beneficial sulfur-oxidizing bacteria located within specialized gill cells known as bacteriocytes. Most previous research has focused on the symbionts in the gills of these (and other) symbiotic bivalves, often assuming that the symbionts only persistently colonize the gills, at least in the adult stage. We used
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Non-kin interactions between Bacillus subtilis soil isolates limit the spread of swarming deficient cheats ISME J. (IF 10.8) Pub Date : 2024-10-08 Katarina Belcijan Pandur, Barbara Kraigher, Ana Tomac, Polonca Stefanic, Ines Mandic Mulec
Cooperative behaviors in human, animal, and even microbial societies are vulnerable to exploitation. Kin discrimination has been hypothesized to help stabilize cooperation. However, the mechanisms that sustain cooperative behavior remain poorly understood. Here, we investigate the role of kin discrimination in limiting the spread of cheats in adjoining populations during surfactant dependent cooperative
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Trans-aconitic acid assimilation system as a widespread bacterial mechanism for environmental adaptation ISME J. (IF 10.8) Pub Date : 2024-10-03 Cao Zheng, Dingqi Liu, Xinyu Lu, Huijun Wu, Jingyi Hua, Chuang Zhang, Kang Liu, Changchun Li, Jin He, Cuiying Du
The ability of bacteria to use natural carbon sources greatly affects their growth and survival in the environment. Bacteria have evolved versatile abilities to use environmental carbon sources, but their diversity and assimilation pathways remain largely unexplored. Trans-aconitic acid, a geometric isomer of cis-aconitic acid involved in the tricarboxylic acid cycle, has long been considered a natural
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Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere ISME J. (IF 10.8) Pub Date : 2024-10-03 Qian Yang, Yin Zhong, Shi-wei Feng, Ping Wen, Heli Wang, Junhong Wu, Sen Yang, Jie-Liang Liang, Dan Li, Qiong Yang, Nora F Y Tam, Ping’an Peng
Plastic marine debris is known to harbor a unique microbiome (termed the “plastisphere”) that can be important in marine biogeochemical cycles. However, the temporal dynamics in the plastisphere and their implications for marine biogeochemistry remain poorly understood. Here, we characterized the temporal dynamics of nitrifying communities in the plastisphere of plastic ropes exposed to a mangrove
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Simple Porifera holobiont reveals complex interactions between the host, an archaeon, a bacterium, and a phage ISME J. (IF 10.8) Pub Date : 2024-10-03 Alessandro N Garritano, Zhelun Zhang, Yunke Jia, Michelle A Allen, Lilian J Hill, Unnikrishnan Kuzhiumparambil, Cora Hinkley, Jean-Baptiste Raina, Raquel S Peixoto, Torsten Thomas
The basal metazoan phylum, Porifera (sponges), is increasingly used as a model to investigate ecological and evolutionary features of microbe-animal symbioses. However, sponges often host complex microbiomes, which has hampered our understanding of their interactions with their microbial symbionts. Here, we describe the discovery and characterisation of the simplest sponge holobiont reported to date
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Insecticide susceptibility in a planthopper pest increases following inoculation with cultured Arsenophonus ISME J. (IF 10.8) Pub Date : 2024-10-03 Tingwei Cai, Pol Nadal-Jimenez, Yuanyuan Gao, Hiroshi Arai, Chengyue Li, Chunyan Su, Kayla C King, Shun He, Jianhong Li, Gregory D D Hurst, Hu Wan
Facultative vertically transmitted symbionts are a common feature of insects that determine many aspects of their hosts’ phenotype. Our capacity to understand and exploit these symbioses is commonly compromised by the microbes unculturability and consequent lack of genetic tools, an impediment of particular significance for symbioses of pest and vector species. Previous work had established that insecticide
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Leveraging genomic information to predict environmental preferences of bacteria ISME J. (IF 10.8) Pub Date : 2024-10-03 Josep Ramoneda, Michael Hoffert, Elias Stallard-Olivera, Emilio O Casamayor, Noah Fierer
Genomic information is now available for a broad diversity of bacteria, including uncultivated taxa. However, we have corresponding knowledge on environmental preferences (i.e. bacterial growth responses across gradients in oxygen, pH, temperature, salinity, and other environmental conditions) for a relatively narrow swath of bacterial diversity. These limits to our understanding of bacterial ecologies
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High-sugar diet leads to loss of beneficial probiotics in housefly larvae guts ISME J. (IF 10.8) Pub Date : 2024-10-03 Anna Voulgari-Kokota, Francesco Boatta, Ruud Rijkers, Bregje Wertheim, Leo W Beukeboom, Jacintha Ellers, Joana Falcao Salles
The housefly (Musca domestica) is a common insect species with only a few recurrent bacterial taxa in its gut microbiota, because the numerous microbial acquisition routes in its septic habitats can favor transient microbes. Here, we investigated the role of the diet on the microbiota and the developmental success of a housefly strain reared on three substrates. We used a control wheat bran-based substrate
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Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection ISME J. (IF 10.8) Pub Date : 2024-10-01 María Dolores Ramos-Barbero, Clara Gómez-Gómez, Gloria Vique, Laura Sala-Comorera, Lorena Rodríguez-Rubio, Maite Muniesa
The order Crassvirales, which includes the prototypical crAssphage (p-crAssphage), is predominantly associated with humans, rendering it the most abundant and widely distributed group of DNA phages in the human gut. The reported human specificity and wide global distribution of p-crAssphage makes it a promising human fecal marker. However, the specificity for the human gut as well as the geographical
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Biofilms inactivate the free-living stage of Batrachochytrium dendrobatidis, the most destructive pathogen for vertebrate diversity ISME J. (IF 10.8) Pub Date : 2024-09-26 Hugo Sentenac, Dirk S Schmeller, Solène Caubet, Adélaïde Carsin, Rémi Guillet, Jessica Ferriol, Joséphine Leflaive, Adeline Loyau
Emerging infectious diseases threaten biodiversity and human health. Many emerging pathogens have aquatic life stages and all immersed substrates have biofilms on their surface, i.e., communities of microorganisms producing a gelatinous matrix. However, the outcome of the interactions between environmental biofilms and pathogens is poorly understood. Here we demonstrate that biofilms reduce the survival
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Pathogen non-planktonic phases within the urinary tract impact early infection and resistance evolution ISME J. (IF 10.8) Pub Date : 2024-09-26 Michael Raatz, Amanda de Azevedo-Lopes, Karolina Drabik, Arne Traulsen, Bartlomiej Waclaw
Treatment of urinary tract infections and the prevention of their recurrence is a pressing global health problem. In a urinary infection, pathogenic bacteria not only reside in the bladder lumen but also attach to and invade the bladder tissue. Planktonic, attached, and intracellular bacteria face different selection pressures from physiological processes such as micturition, immune response, and antibiotic
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Hidden syndinian and perkinsid infections in dinoflagellate hosts revealed by single-cell transcriptomics ISME J. (IF 10.8) Pub Date : 2024-09-26 Elizabeth C Cooney, Brian S Leander, Patrick J Keeling
Free-living core dinoflagellates are commonly infected by members of two parasitic clades that are themselves closely related to dinoflagellates, the marine alveolates and perkinsids. These parasites are abundant and ecologically important, but most species have been difficult to observe directly or cultivate, so our knowledge of them is usually restricted to environmental 18S rRNA gene sequences,
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Arbuscular mycorrhizal hyphae facilitate rhizobia dispersal and nodulation in legumes ISME J. (IF 10.8) Pub Date : 2024-09-26 Jiadong He, Lin Zhang, Judith Van Dingenen, Sandrien Desmet, Sofie Goormachtig, Maryline Calonne-Salmon, Stéphane Declerck
In soil ecosystems, rhizobia occupy the rhizosphere of legume roots to form nodules, a process triggered by microbial recognition of specific root-derived signals (i.e., flavonoids). However, soil conditions can limit bacterial motility, restricting signal perception to the area directly influenced by roots. Legumes, like most plants of agricultural interest, associate with arbuscular mycorrhizal fungi
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Niche breadth specialisation impacts ecological and evolutionary adaptation following environmental change ISME J. (IF 10.8) Pub Date : 2024-09-26 Cécile Gubry-Rangin, Axel Aigle, Leonel Herrera-Alsina, Lesley T Lancaster, James I Prosser
None declared.Conflicts of interestEcological theory predicts that organismal distribution and abundance depend on the ability to adapt to environmental change. It also predicts that eukaryotic specialists and generalists will dominate in extreme environments or following environmental change, respectively. This theory has attracted little attention in prokaryotes, especially in archaea, which drive
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Idiosyncratic genome evolution of the thermophilic cyanobacterium Synechococcus at the limits of phototrophy ISME J. (IF 10.8) Pub Date : 2024-09-25 C Logan Pierpont, Jacob J Baroch, Matthew J Church, Scott R Miller
Thermophilic microorganisms are expected to have smaller cells and genomes compared with mesophiles, a higher proportion of horizontally acquired genes, and distinct nucleotide and amino acid composition signatures. Here, we took an integrative approach to investigate these apparent correlates of thermophily for Synechococcus A/B cyanobacteria, which include the most heat-tolerant phototrophs on the
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Spatiotemporal dynamics of giant viruses within a deep freshwater lake reveal a distinct dark-water community ISME J. (IF 10.8) Pub Date : 2024-09-23 Liwen Zhang, Lingjie Meng, Yue Fang, Hiroyuki Ogata, Yusuke Okazaki
Giant viruses significantly regulate the ecological dynamics of diverse ecosystems. Although metagenomics has expanded our understanding of their diversity and ecological roles played in marine environments, little is known about giant viruses of freshwater ecosystems. Most previous studies have employed short-read sequencing and therefore resulted in fragmented genomes, hampering accurate assessment
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Predatory protists impact plant performance by promoting plant growth-promoting rhizobacterial consortia ISME J. (IF 10.8) Pub Date : 2024-09-23 Sai Guo, Stefan Geisen, Yani Mo, Xinyue Yan, Ruoling Huang, Hongjun Liu, Zhilei Gao, Chengyuan Tao, Xuhui Deng, Wu Xiong, Qirong Shen, George A Kowalchuk, Rong Li
Plant performance is impacted by rhizosphere bacteria. These bacteria are subjected to both bottom-up control by root exudates as well as top-down control by predators, particularly protists. Protists stimulate plant growth-promoting microbes resulting in improved plant performance. However, knowledge of the mechanisms that determine the interconnections within such tripartite protist–bacteria–plant
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Abiotic factors shape mosquito microbiomes that enhance host development ISME J. (IF 10.8) Pub Date : 2024-09-23 Nicola G Kriefall, Priscilla S Seabourn, Nicole M Yoneishi, Kahiwahiwa Davis, Kirsten K Nakayama, Danya E Weber, Nicole A Hynson, Matthew C I Medeiros
Metazoans rely on interactions with microorganisms through multiple life stages. For example, developmental trajectories of mosquitoes can vary depending on the microorganisms available during their aquatic larval phase. However, the role that the local environment plays in shaping such host-microbe dynamics and the consequences for the host organism remain inadequately understood. Here, we examine
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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
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
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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
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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
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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
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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
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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
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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
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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
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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