FEMS Microbiology Ecology

Ciuchcinski, Karol; Stokke, Runar; Steen, Ida Helene; Dziewit, Lukasz

doi: 10.1093/femsec/fiae124pmid: 39271469

Plasmids are one of the key drivers of microbial adaptation and evolution. However, their diversity and role in adaptation, especially in extreme environments, remains largely unexplored. In this study, we aimed to identify, characterize, and compare plasmid sequences originating from samples collected from deep-sea hydrothermal vents located in Arctic Mid-Ocean Ridges. To achieve this, we employed, and benchmarked three recently developed plasmid identification tools—PlasX, GeNomad, and PLASMe—on metagenomic data from this unique ecosystem. To date, this is the first direct comparison of these computational methods in the context of data from extreme environments. Upon recovery of plasmid contigs, we performed a multiapproach analysis, focusing on identifying taxonomic and functional biases within datasets originating from each tool. Next, we implemented a majority voting system to identify high-confidence plasmid contigs, enhancing the reliability of our findings. By analysing the consensus plasmid sequences, we gained insights into their diversity, ecological roles, and adaptive significance. Within the high-confidence sequences, we identified a high abundance of Pseudomonadota and Campylobacterota, as well as multiple toxin–antitoxin systems. Our findings ensure a deeper understanding of how plasmids contribute to shaping microbial communities living under extreme conditions of hydrothermal vents, potentially uncovering novel adaptive mechanisms.

Liu, Xiangyu; Fernandes, Hocelayne Paulino; Ossowicki, Adam; Vrieling, Klaas; Lommen, Suzanne T E; Bezemer, Thiemo Martijn

doi: 10.1093/femsec/fiae116pmid: 39174482

Plant-associated microorganisms can negatively influence plant growth, which makes them potential biocontrol agents for weeds. Two Gammaproteobacteria, Serratia plymuthica and Pseudomonas brassicacearum, isolated from roots of Jacobaea vulgaris, an invasive weed, negatively affect its root growth. We examined whether the effects of S. plymuthica and P. brassicacearum on J. vulgaris through root inoculation are concentration-dependent and investigated if these effects were mediated by metabolites in bacterial suspensions. We also tested whether the two bacteria negatively affected seed germination and seedling growth through volatile emissions. Lastly, we investigated the host specificity of these two bacteria on nine other plant species. Both bacteria significantly reduced J. vulgaris root growth after root inoculation, with S. plymuthica showing a concentration-dependent pattern in vitro. The cell-free supernatants of both bacteria did not affect J. vulgaris root growth. Both bacteria inhibited J. vulgaris seed germination and seedling growth via volatiles, displaying distinct volatile profiles. However, these negative effects were not specific to J. vulgaris. Both bacteria negatively affect J. vulgaris through root inoculation via the activity of bacterial cells, while also producing volatiles that hinder J. vulgaris germination and seedling growth. However, their negative effects extend to other plant species, limiting their potential for weed control.

Ho, Lisim; Lai, Chengyu; Daim, Leona D J; Noh, Normahnani M; Yap, Yunci; Ibrahim, Julia; Teh, Cheekeng

doi: 10.1093/femsec/fiae122pmid: 39264053

Understanding the microbial communities in asymptomatic oil palm seedlings is crucial for developing disease-suppressive microbiota against basal stem rot (BSR) in oil palm. In this study, we compared the microbial communities in bulk soil, rhizosphere, and endosphere of control, asymptomatic, and symptomatic seedlings following inoculation with Ganoderma boninense. Our findings revealed significant shifts in microbial structure and interactions, particularly in asymptomatic seedlings. Both Actinobacteriota and Ascomycota were notably enriched in these samples, with Actinobacteriota identified as keystone taxa. Long-read shotgun metagenomics demonstrated that 67.4% of enriched Actinobacteriota taxa were unique to asymptomatic seedlings. Similarly, Ascomycota members showed significant enrichment, suggesting their potential role in BSR suppression. The consistent identification of these phyla across various analyses underscores their importance in disease resistance. This is the first report detailing the shifts in prokaryotic and fungal communities in asymptomatic and symptomatic seedlings, offering insights into potential disease-suppressive taxa across three compartments: bulk soil, rhizosphere, and endosphere of oil palm seedlings.

Gloder, Gabriele; Bourne, Mitchel E; Cuny, Maximilien A C; Verreth, Christel; Crauwels, Sam; Dicke, Marcel; Poelman, Erik H; Jacquemyn, Hans; Lievens, Bart

doi: 10.1093/femsec/fiae115pmid: 39165109

There is increasing evidence that host–parasitoid interactions can have a pronounced impact on the microbiome of host insects, but it is unclear to what extent this is caused by the host and/or parasitoid. Here, we compared the internal and external microbiome of caterpillars of Pieris brassicae and Pieris rapae parasitized by Cotesia glomerata or Cotesia rubecula with nonparasitized caterpillars. Additionally, we investigated the internal and external microbiome of the parasitoid larvae. Both internal and external bacterial densities were significantly higher for P. brassicae than P. rapae, while no differences were found between parasitized and nonparasitized caterpillars. In contrast, parasitism significantly affected the composition of the internal and external microbiome of the caterpillars and the parasitoid larvae, but the effects were dependent on the host and parasitoid species. Irrespective of host species, a Wolbachia species was exclusively found inside caterpillars parasitized by C. glomerata, as well as in the corresponding developing parasitoid larvae. Similarly, a Nosema species was abundantly present inside parasitized caterpillars and the parasitoid larvae, but this was independent of the host and the parasitoid species. We conclude that parasitism has pronounced effects on host microbiomes, but the effects depend on both the host and parasitoid species.

Mazorra-Alonso, Mónica; Peralta-Sánchez, Juan Manuel; Heeb, Philipp; Jacob, Staffan; Martin-Vivaldi, Manuel; Martínez-Bueno, Manuel; Núñez-Gómez, Rafael; Sacristán-Soriano, Oriol; Soler, Juan José

doi: 10.1093/femsec/fiae106pmid: 39049462

Bacteria have been suggested as being partially responsible for avian nest odours and, thus, volatiles from their metabolism could influence the intensity of selection pressures due to parasites detecting olfactory cues of their hosts. Here, we tested this hypothesis by exploring intraspecific and interspecific variability in microbial environments, volatile profiles and intensity of ectoparasitism by Carnus hemapterus in the nests of 10 avian species. As expected, we found that (i) alpha and beta diversity of microbial and volatile profiles were associated with each other. Moreover, (ii) alpha diversity of bacteria and volatiles of the nest environment, as well as some particular bacteria and volatiles, was associated with the intensity of parasitism at early and late stages of the nestling period. Finally, (iii) alpha diversity of the nest microbiota, as well as some particular bacteria and volatiles, was correlated with fledging success. When considering them together, the results support the expected links between the microbial environment and nest odours in different bird species, and between the microbial environment and both ectoparasitism intensity and fledging success. Relative abundances of particular volatiles and bacteria predicted ectoparasitism and/or fledging success. Future research should prioritise experimental approaches directed to determine the role of bacteria and volatiles in the outcomes of host–ectoparasite interactions.

Gekenidis, Maria-Theresia; Vollenweider, Vera; Joyce, Aoife; Murphy, Sinéad; Walser, Jean-Claude; Ju, Feng; Bürgmann, Helmut; Hummerjohann, Jörg; Walsh, Fiona; Drissner, David

doi: 10.1093/femsec/fiae118pmid: 39216995

Fresh produce is suggested to contribute highly to shaping the gut resistome. We investigated the impact of pig manure and irrigation water quality on microbiome and resistome of field-grown lettuce over an entire growth period. Lettuce was grown under four regimes, combining soil amendment with manure (with/without) with sprinkler irrigation using river water with an upstream wastewater input, disinfected by UV (with/without). Lettuce leaves, soil, and water samples were collected weekly and analysed by bacterial cultivation, 16S rRNA gene amplicon sequencing, and shotgun metagenomics from total community DNA. Cultivation yielded only few clinically relevant antibiotic-resistant bacteria (ARB), but numbers of ARB on lettuce increased over time, while no treatment-dependent changes were observed. Microbiome analysis confirmed a temporal trend. Antibiotic resistance genes (ARGs) unique to lettuce and water included multidrug and β-lactam ARGs, whereas lettuce and soil uniquely shared mainly glycopeptide and tetracycline ARGs. Surface water carried clinically relevant ARB (e.g. ESBL-producing Escherichia coli or Serratia fonticola) without affecting the overall lettuce resistome significantly. Resistance markers including biocide and metal resistance were increased in lettuce grown with manure, especially young lettuce (increased soil contact). Overall, while all investigated environments had their share as sources of the lettuce resistome, manure was the main source especially on young plants. We therefore suggest minimizing soil–vegetable contact to minimize resistance markers on fresh produce.

Taylor, Lois S; Mason, Allison R; Noel, Hannah L; Essington, Michael E; Davis, Mary C; Brown, Veronica A; Steadman, Dawnie W; DeBruyn, Jennifer M

doi: 10.1093/femsec/fiae119pmid: 39293810

Human decomposition in terrestrial ecosystems is a dynamic process creating localized hot spots of soil microbial activity. Longer-term (beyond a few months) impacts on decomposer microbial communities are poorly characterized and do not typically connect microbial communities to biogeochemistry, limiting our understanding of decomposer communities and their functions. We performed separate year-long human decomposition trials, one starting in spring, another in winter, integrating bacterial and fungal community structure and abundances with soil physicochemistry and biogeochemistry to identify key drivers of microbial community change. In both trials, soil acidification, elevated microbial respiration, and reduced soil oxygen concentrations occurred. Changes in soil oxygen concentrations were the primary driver of microbial succession and nitrogen transformation patterns, while fungal community diversity and abundance was related to soil pH. Relative abundance of facultative anaerobic taxa (Firmicutes and Saccharomycetes) increased during the period of reduced soil oxygen. The magnitude and timing of the decomposition responses were amplified during the spring trial relative to the winter, even when corrected for thermal inputs (accumulated degree days). Further, soil chemical parameters, microbial community structure, and fungal gene abundances remained altered at the end of 1 year, suggesting longer-term impacts on soil ecosystems beyond the initial pulse of decomposition products.

Salmaso, Nico; Cerasino, Leonardo; Pindo, Massimo; Boscaini, Adriano

doi: 10.1093/femsec/fiae117pmid: 39227168

Untargeted genetic approaches can be used to explore the high metabolic versatility of cyanobacteria. In this context, a comprehensive metagenomic shotgun analysis was performed on a population of Dolichospermum lemmermannii collected during a surface bloom in Lake Garda in the summer of 2020. Using a phylogenomic approach, the almost complete metagenome-assembled genome obtained from the analysis allowed to clarify the taxonomic position of the species within the genus Dolichospermum and contributed to frame the taxonomy of this genus within the ADA group (Anabaena/Dolichospermum/Aphanizomenon). In addition to common functional traits represented in the central metabolism of photosynthetic cyanobacteria, the genome annotation uncovered some distinctive and adaptive traits that helped define the factors that promote and maintain bloom-forming heterocytous nitrogen-fixing Nostocales in oligotrophic lakes. In addition, genetic clusters were identified that potentially encode several secondary metabolites that were previously unknown in the populations evolving in the southern Alpine Lake district. These included geosmin, anabaenopetins, and other bioactive compounds. The results expanded the knowledge of the distinctive competitive traits that drive algal blooms and provided guidance for more targeted analyses of cyanobacterial metabolites with implications for human health and water resource use.

Freixa, Anna; González-Trujillo, Juan David; Sacristán-Soriano, Oriol; Borrego, Carles M; Sabater, Sergi

doi: 10.1093/femsec/fiae126pmid: 39277783

Bacterial communities in river sediments are shaped by a trade-off between dispersal from upstream or nearby land and selection by the local environmental conditions. In temporary rivers (i.e. those characterized by long drying periods and subsequent rewetting) seasonal hydrological dynamics shape bacterial communities by connecting or disconnecting different river habitats. In this study, we tracked and compared the temporal and spatial changes in the composition of bacterial communities in streambed sediments and floodplain habitats across both permanent and intermittent river segments. Our findings revealed that environmental selection played a key role in assembling bacterial communities in both segments. We argue that distinct environmental features act as filters at the local scale, favoring specific bacterial taxa in isolated pools and promoting some typically terrestrial taxa in dry areas. Considering the prospective extension of drying intervals due to climate change, our results suggest an emerging trend wherein bacterial assemblages in temporary streams progressively incorporate microorganisms of terrestrial origin, well-adapted to tolerate desiccation phases. This phenomenon may constitute an integral facet of the broader adaptive dynamics of temporary river ecosystems in response to the impacts of climate change.

Chase, Emily E; Truchon, Alexander R; Creasey, Brooke A; Wilhelm, Steven W

doi: 10.1093/femsec/fiae123pmid: 39271456

Aureococcus anophagefferens forms a model host-virus system with the “giant virus” Kratosvirus quantuckense. Studies to define its ribocell (uninfected) and virocell (virus-infected) forms are needed as these states co-occur during algal blooms. Previously, a link between light-derived energy, virus particle production, and virocell formation was noted. We explored how the time of day (morning, midday, or late day) of virus-host contact shaped virocell ontogeny. In parallel, we explored the dependence on light-derived energy in this mixotrophic plankter by inhibiting photosystem II, testing the role of heterotrophic energy in infection dynamics. Using flow cytometry and photochemical assessments, we examined the physiology of infected cells and controls, and estimated virus particle production. We observed differences between ribocell and virocell response to treatments, including reductions in virus particle production during reduced light duration) and PSII inhibition (i.e. “forced heterotrophy”). This work demonstrates the importance of light in shaping the fate of infected cells and provides insight into factors that constrain in situ blooms. Most significantly, we show that time of the solar day when a virus and host come into contact influences viral particle production, and therefore bloom dynamics; a factor that needs to be considered in bloom modeling work.