Eelgrass microbiome and disease dynamics under field and lab heat stress.

Successive stressors alter microbiome composition and reduce resilience in the eelgrass Zostera marina.

The microbiomes of host organisms and their direct source environments are closely linked and key for shaping microbial community dynamics. The relationship between these linked dynamics is largely unexplored because source substrates are usually unavailable. To address this current knowledge gap, we employed bacteriovorous Caenorhabditis nematodes as a unique model system, for which source substrates like rotting apples can be easily collected. We compared single host microbiomes with their corresponding apple source substrates, as well as nematode-free substrates, over a 2-year sampling period in the botanical garden in Kiel, Germany. We found that single worms have unique microbiomes, which overlap most strongly with nematodes from the same source apple. A comparison to previous, related work revealed that variation in microbiome composition of natural Caenorhabditis isolates is significantly influenced by the substrate type, from which worms were obtained (e.g., fruits or compost). Our current sampling further showed that microbiome assembly is mostly driven by dispersal limitation. Importantly, two independent analysis approaches consistently suggest that worm microbiomes significantly influence characteristics of the apple microbiomes, possibly indicating niche construction by nematodes. Moreover, combining apple microbiome and metabolome data, we identified individual microbes and specific compounds indicative of fruit ripening that are significantly associated with nematode presence. In conclusion, our study elucidates the complex relationship between host microbiomes and their directly connected substrate microbiomes. Our analyses underscore the significant influence of nematode microbiomes on shaping the apple microbiome and, consequently, the fruit's metabolic capacity, thereby enhancing our general understanding of host-microbiome interactions in their natural habitat.IMPORTANCEAlmost all complex organisms are host to a microbial community, the microbiome. This microbiome can influence diverse host functions, such as food processing, protection against parasites, or development. The relationship between host and microbiome critically depends on the assembly of the microbial community, which may be shaped by microbes in the directly linked environment, the source microbiome. This assembly process is often not well understood because of the unavailability of source substrates. Here, we used Caenorhabditis nematodes as a model system that facilitates a direct comparison of host and source microbiomes. Based on a 2-year sampling period, we identified (i) a clear link between assembly dynamics of host and source microbiomes, (ii) a significant influence of nematode microbiomes on apple microbiomes, and (iii) specific microbes and compounds that are associated with the presence of nematodes in the sampled substrates. Overall, our study enhances our understanding of microbiome assembly dynamics and resulting functions.

Compositional shifts in the strawberry fruit microbiome in response to near-harvest application of Metschnikowia fructicola, a yeast biocontrol agent

Early blight, caused by Alternaria solani, along with brown spot, caused by A. alternata, have the potential to reduce quality and yield in potato production globally. Prior to this study, the incidence, disease impact, and fungicide resistance attributes of A. alternata in Wisconsin were poorly understood. Potato pathogens were isolated from foliar lesions at three commercial locations in Wisconsin in 2012 and 2017 and were initially morphologically identified as A. solani (n = 33) and A. alternata (n = 40). Identifications were further corroborated with the phylogenetic analysis of the internal transcribed spacer (ITS), translation elongation factor 1 (TEF1), gapdh, Alt a 1, and OPA10-2. A multigene phylogeny of ITS, TEF1, gapdh, and Alt a 1 showed five genotypes of A. alternata and one single genotype of A. solani. We demonstrated that the A. alternata isolates were virulent on potato cultivars Russet Burbank (P < 0.013) and Atlantic (P < 0.0073), though they caused less disease than A. solani (P < 0.0001 and P < 0.0001, respectively). A. alternata caused little disease on the breeding line 24-24-12 (P = 0.9929), and A. solani caused fewer disease symptoms on 24-24-12 than on Russet Burbank (P < 0.0001) or Atlantic (P < 0.0001). Breeding line 24-24-12 may be a promising source of potential resistance for the two diseases. There was no significant difference in virulence of different A. alternata genotypes, and no significant difference in virulence or genotype clustering among isolates from the three locations. Isolates of A. alternata that induced chlorosis caused larger lesion areas than isolates that did not in Russet Burbank (P < 0.0001), Atlantic (P < 0.0001), and 24-24-12 (P = 0.0365). There was no significant difference in virulence between quinone outside inhibitor (QoI)-sensitive and QoI-resistant isolates of A. alternata. This study enhanced our understanding of potato early blight and brown spot in Wisconsin, and suggested that A. alternata in addition to A. solani should be carefully monitored and possibly uniquely managed in order to achieve overall disease control.

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 420:277-281 (2010) - DOI: https://doi.org/10.3354/meps08873 NOTE Functional diversity in amphipods revealed by stable isotopes in an eelgrass ecosystem J. P. Farlin1,*, L. S. Lewis1,2, T. W. Anderson1, C. T. Lai1 1 Department of Biology and Coastal & Marine Institute, San Diego State University, 5500 Campanile Drive, San Diego, California 92182-4614, USA 2Present address: Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, California 92083-0202, USA *Email: nilraf@gmail.com ABSTRACT: Amphipods are often dominant components of benthic marine communities and may exhibit taxon-specific differences in feeding behavior. As a result, variation in the composition of amphipod communities is an important metric for the interpretation of trophic dynamics in benthic marine ecosystems. Though previous studies of amphipod diets indicate functional diversity among taxa, few studies have examined whether these differences are detectible using time-integrated natural tracers of in situ feeding habits. We used stable isotope ratios of nitrogen (δ15N) and carbon (δ13C) to examine trophic structure among amphipod taxa belonging to 5 families in an eelgrass (Zostera marina) ecosystem in San Diego Bay, California. The relative contribution of sources of primary production to amphipod diets was further analyzed using a mixing model bracketed by 2 dominant sources of primary production in the system: eelgrass and algae. We detected significant differences in both δ13C and δ15N among amphipod taxa, indicating family-specific differences in feeding habits that generally agree with previous studies of amphipod diets. Hyalids fed almost exclusively on eelgrass, ischyrocerids and ampithoids tended to feed more on algae and eelgrass, respectively, and caprellids exhibited heterogeneous feeding on both algae and eelgrass. The relatively high δ15N value of oedicerotids suggested that this group was likely carnivorous. Our findings are in general agreement with previous descriptions of family-specific amphipod feeding behaviors, suggesting that stable isotopes are a useful tool for describing the functional roles of mesograzers in eelgrass ecosystems. KEY WORDS: Functional diversity · Stable isotopes · Eelgrass food web · Amphipods · Amphipod feeding Full text in pdf format PreviousNextCite this article as: Farlin JP, Lewis LS, Anderson TW, Lai CT (2010) Functional diversity in amphipods revealed by stable isotopes in an eelgrass ecosystem. Mar Ecol Prog Ser 420:277-281. https://doi.org/10.3354/meps08873 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 420. Online publication date: December 16, 2010 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2010 Inter-Research.

Marine diatoms contribute significantly to global oceanic primary production, constituting ~25% of earth production but are susceptible to the impacts of ocean warming. While organisms’ adaptation to rising temperatures may mitigate these impacts, it could also disrupt species interactions, including those between hosts and their microbiomes. In our study, we examined thermal performance and diversity changes in the microbiome of the tropical diatom Chaetoceros tenuissimus after long-term adaptation to ambient (LA) and warming (LW) temperatures. We observed notable shifts in the metabolomic profile, with amino acids accumulating after LW adaptation and sugars accumulating after LA, while lipids content remained unchanged. After LW, the microbiota increased maximum growth rate without changing its temperature optimum. Roseovarius sp. dominated the microbiome community at both LA (49.6%) and LW strains (42.8%) proving a strong partnership. Extinctions were highest under warming occurring in the low-abundant genera, but different partners developed increasing richness, with changes induced in the core microbiome. Short-term warming, however, resulted in decreased richness. Beta diversity was associated with long-term adaptation instead of assay temperature. Our findings align with general plant species association models, suggesting that long-term evolution of mutualisms enhances diversity and strength, particularly under warming in the marine partnership studied here. Our experimental results highlight the importance of examine long-term coevolution of host- microbiome partnerships to improve our understanding of consequences of warming.

Background Kingella kingae, a normal component of the upper respiratory flora, is being increasingly recognized as an important invasive pathogen in young children. Genetic diversity of this species has not been studied.MethodsWe analyzed 103 strains from different countries and clinical origins by a new multilocus sequence-typing (MLST) schema. Putative virulence gene rtxA, encoding an RTX toxin, was also sequenced, and experimental virulence of representative strains was assessed in a juvenile-rat model.ResultsThirty-six sequence-types (ST) and nine ST-complexes (STc) were detected. The main STc 6, 14 and 23 comprised 23, 17 and 20 strains respectively, and were internationally distributed. rtxA sequencing results were mostly congruent with MLST, and showed horizontal transfer events. Of interest, all members of the distantly related ST-6 (n = 22) and ST-5 (n = 4) harboured a 33 bp duplication or triplication in their rtxA sequence, suggesting that this genetic trait arose through selective advantage. The animal model revealed significant differences in virulence among strains of the species.ConclusionMLST analysis reveals international spread of ST-complexes and will help to decipher acquisition and evolution of virulence traits and diversity of pathogenicity among K. kingae strains, for which an experimental animal model is now available.

The human skin microbiome plays a crucial role in maintaining skin health by acting as a barrier against pathogens and modulating immune regulation. This case study investigates the skin microbiome of two healthy Korean male individuals in their 20s during Antarctic expeditions, focusing on microbial changes, reversion to pre-expedition states, and the influence of environmental and lifestyle factors. Notable microbial alterations were observed, including increases in Pseudomonadota and decreases in Actinomycetota, indicating pronounced microbial shifts in response to harsh environmental factors such as low temperature and humidity. Post-expedition revealed incomplete recovery to pre-expedition states, with Host A showing a higher resilience index, suggesting faster microbial recovery. Correlation analyses revealed associations between microbial changes and environmental factors (e.g., temperature, humidity, atmospheric pressure) as well as lifestyle factors (e.g., sunblock usage, outdoor activities), highlighting complex interactions between host behaviors and microbiome dynamics. Despite the study’s limited sample size, these findings offer insights into the adaptability and resilience of the skin microbiome under extreme environments, with potential implications for health management and skincare strategies during isolated and prolonged expeditions.

Three taxa, Colletotrichum orbiculare, the unconfirmed teleomorph of C. orbiculare (Glomerella cingulata var. orbiculare), and C. magna, have been reported to cause anthracnose of cucurbits. In a previous study, virulence, vegetative compatibility, and mtDNA RFLPs have been used to examine these taxa. The three taxa can be distinguished based on mtDNA RFLPs. Under controlled greenhouse inoculation tests, only isolates of C. orbiculare (CO) from cucurbit hosts were highly virulent on cucurbit foliage; isolates of G. cingulata (GC) and C. magna (CM), and CO from cocklebur hosts were weakly virulent or avirulent. The majority of CM and GC isolates were recovered from fruit, whereas most CO isolates were recovered from foliage. A study was conducted to evaluate the pathogenicity and virulence of anthracnose isolates on cucurbit fruit. Twenty-seven isolates of the three taxa were selected based on the host and geographic origin, mtDNA RFLP haplotype, vegetative compatibility group, and race. Mature fruit from cucumber cultivars Marketer (susceptible) and H19 (resistant) and watermelon cultivars Black Diamond (susceptible) and Charleston Gray (resistant) were used. Fruit were inoculated by placing Torula yeast agar inoculum plugs (8mm in diameter) into wounds. Following inoculation, the wounds were covered with Parafilm and incubated for 8 days at 25C at 100% RH. On the third day the Parafilm was removed from the wound. Disease symptoms were evaluated by measuring lesion diameter and depth and evaluating the presence or absence of sporulation. All three anthracnose taxa are capable of infecting cucurbit fruit. CM and GC isolates were more virulent than CO isolates on cucumber. In contrast, on `Black Diamond', CO isolates were more virulent than CM and GC isolates. No significant differences in virulence were observed on `Charleston Gray'. There were no significant differences in virulence between the races of CO except on `Charleston Gray', where race 2 isolates were significantly more virulent than race 1. CO isolates from cocklebur were only weakly virulent on cucurbit fruit.

In this study, we compared the virulence of the most common serovars of Glaesserella parasuis in China, serovars 4, 5, 12, and 13 (36 strains in total) in BALB/c mice and piglets. In mice, the median lethal doses (LD50s) of the four serovars were roughly 9.80 × 107–4.60 × 109 CFU, 2.10 × 108–8.85 × 109 CFU, 4.81 × 107–7.01 × 109 CFU, and 1.75 × 108–8.45 × 108 CFU, respectively. Serovar 13 showed the strongest virulence, followed by serovar 4, serovar 12, and serovar 5, but a significant difference in virulence was only observed between serovars 5 and 13. The virulence of strains of the same serovars differed significantly in piglets. Virulent and attenuated strains were present in all serovars, but serovar 5 was the most virulent in piglets, followed by serovars 13, 4, and 12. A significant difference in virulence was observed between serovars 5 and 4 and between serovars 5 and 12. However, the virulence of serovars 5 and 13 did not differ significantly. This comprehensive analysis of G. parasuis virulence in mice and piglets demonstrated that: (1) the order of virulence of the four domestic epidemic serovars (from strongest to weakest) in piglets was serovars 5, 13, 4, and 12; (2) both virulent and attenuated strains were present in all serovars, so virulence did not necessarily correlate with serovar; (3) Although G. parasuis was fatal in BALB/c mice, its virulence is inconsistent with that in piglets, indicating that BALB/c mice are inadequate as an alternative model of G. parasuis infection.

Tenebrio molitor (Coleoptera: Tenebrionidae) as an alternative host for the study of pathogenicity in Candida auris

ABSTRACTChikungunya virus (CHIKV) is a reemerging arbovirus capable of causing explosive outbreaks of febrile illness, polyarthritis, and polyarthralgia, inflicting severe morbidity on affected populations. CHIKV can be genetically classified into 3 major lineages: West African (WA); East, Central, and South African (ECSA); Indian Ocean (IOL); and Asian. Additionally, the Indian Ocean (IOL) sublineage emerged within the ECSA clade and the Asian/American sublineage emerged within the Asian clade. While differences in epidemiological and pathological characteristics among outbreaks involving different CHIKV lineages and sublineages have been suggested, few targeted investigations comparing lineage virulence levels have been reported. We compared the virulence levels of CHIKV isolates representing all major lineages and sublineages in the type I interferon receptor-knockout A129 mouse model and found lineage-specific differences in virulence. We also evaluated the cross-protective efficacy of the IOL-derived, live-attenuated vaccine strain CHIKV/IRESv1 against the Asian/American CHIKV isolate YO123223 in both murine and nonhuman primate models, as well as the WA strain SH2830 in a murine model. The CHIKV/IRES vaccine provided protection both in mice and in nonhuman primate cohorts against Caribbean strain challenge and protected mice against WA challenge. Taken together, our data suggest that Asian/American CHIKV strains are less virulent than those in the Asian, ECSA, and WA lineages and that despite differences in virulence, IOL-based vaccine strains offer robust cross-protection against strains from other lineages. Further research is needed to elucidate the genetic basis for variation in CHIKV virulence in the A129 mouse model and to corroborate this variation with human pathogenicity.

BackgroundThe parasite Hematodinium sp. causes morbidity and seasonal mortality events in more than 40 decapod species globally and therefore, it is now recognised as a significant threat to the future sustainability of shellfish fisheries and aquaculture worldwide. Among these, Norway lobster (Nephrops norvegicus), an important representative of the marine benthos and supporting the most valuable shellfish fishery in the UK, experience yearly seasonal Hematodinium sp. patent infections. Currently, little is known about the N. norvegicus microbiome and potential role during Hematodinium sp. infection. Therefore, in this study we investigated the microbiome dynamics of N. norvegicus associated with Hematodinium sp. infection and disease progression in the haemolymph and gut. N. norvegicus were sampled from the Clyde Sea Area, Scotland during the peak of the Hematodinium sp. patent infection. The presence and intensity of Hematodinium sp. infection were determined using the body colour method (BCM), pleopod method (PM), histology (heart, gonads, hepatopancreas, gills and muscle) and molecular tools (PCR).ResultsMarked shifts in the bacterial richness of the haemolymph and significant alterations in the overall bacterial community composition of both tissues were observed in infected lobsters. These changes, observed even at subpatent levels of infection (only positive by PCR), indicate a prompt and persistent microbiome shift associated with Hematodinium sp. infection. Furthermore, smaller healthy animals (25.2 ± 1.20 mm CL) known to be particularly susceptible to high severity infection displayed a decreased microbiome richness in the haemolymph suggesting a potential link between the host microbiome and susceptibility to disease progression, a possibility that merits further research.ConclusionsThis study offers the first insights into the pathobiome of N. norvegicus due to Hematodinium sp. infection and disease that in turn provides a foundation for further studies on the pathogenesis of this important parasitic disease.

Rationale:Viral infection of the respiratory tract can be associated with propagating effects on the airway microbiome, and microbiome dysbiosis may influence viral disease.Objective:To define the respiratory tract microbiome in COVID-19 and relationship disease severity, systemic immunologic features, and outcomes.Methods and Measurements:We examined 507 oropharyngeal, nasopharyngeal and endotracheal samples from 83 hospitalized COVID-19 patients, along with non-COVID patients and healthy controls. Bacterial communities were interrogated using 16S rRNA gene sequencing, commensal DNA viruses Anelloviridae and Redondoviridae were quantified by qPCR, and immune features were characterized by lymphocyte/neutrophil (L/N) ratios and deep immune profiling of peripheral blood mononuclear cells (PBMC).Main Results:COVID-19 patients had upper respiratory microbiome dysbiosis, and greater change over time than critically ill patients without COVID-19. Diversity at the first time point correlated inversely with disease severity during hospitalization, and microbiome composition was associated with L/N ratios and PBMC profiles in blood. Intubated patients showed patient-specific and dynamic lung microbiome communities, with prominence of Staphylococcus. Anelloviridae and Redondoviridae showed more frequent colonization and higher titers in severe disease. Machine learning analysis demonstrated that integrated features of the microbiome at early sampling points had high power to discriminate ultimate level of COVID-19 severity.Conclusions:The respiratory tract microbiome and commensal virome are disturbed in COVID-19, correlate with systemic immune parameters, and early microbiome features discriminate disease severity. Future studies should address clinical consequences of airway dysbiosis in COVID-19, possible use as biomarkers, and role of bacterial and viral taxa identified here in COVID-19 pathogenesis.

Microbiome Shifts in Peri-Implantitis: Longitudinal Characterization of Dysbiosis and Resolution