Association of host and microbial species diversity across spatial scales in desert rodent communities

Microbial mutualism promoting the coexistence of competing species: Double-layer model for two competing hosts and one microbial species

Gause's law of competitive exclusion holds that the coexistence of competing species is extremely unlikely when niches are not differentiated. This law is supported by many mathematical studies, yet the coexistence of competing species is nearly ubiquitous in real ecosystems. We pay attention to the fact that plants and animals usually contact with microbial species as mutualistic partners. The activity spaces of host species are different from those of micro-organisms. In the present study, we apply double-layer model to the association of two competing hosts and a microorganism. Two lattices are prepared: one is for hosts, and the other is for microorganism. The basic equation obtained by mean-field theory is an extension of Lotka-Volterra competition model. Both mathematical analysis and numerical simulations reveal that a shared microbial mutualist can permit the coexistence of competing hosts. From the derived condition of coexistence, we believe the microbial mutualism promotes biodiversity in many ecological systems.

Bacterial diversity in Icelandic cold spring sources and in relation to the groundwater amphipod Crangonyx islandicus

Crangonyx islandicus is a groundwater amphipod endemic to Iceland, considered to have survived the Ice Ages in subglacial refugia. Currently the species is found in spring sources in lava fields along the tectonic plate boundary of the country. The discovery of a groundwater species in this inaccessible habitat indicates a hidden ecosystem possibly based on chemoautotrophic microorganisms as primary producers. To explore this spring ecosystem, we assessed its microbial diversity and analysed whether and how the diversity varied between the amphipods and the spring water, and if was dependent on environmental factors and geological settings. Isolated DNA from spring water and from amphipods was analysed using metabarcoding methods, targeting the 16S rRNA gene. Two genera of bacteria, Halomonas and Shewanella were dominating in the amphipod samples in terms of relative abundance, but not in the groundwater samples where Flavobacterium, Pseudomonas and Alkanindiges among others were dominating. The richness of the bacteria taxa in the microbial community of the groundwater spring sources was shaped by pH level and the beta diversity was shaped by geographic locations.

The dynamics between limited-term and lifelong coinfecting bacterial parasites in wild rodent hosts

Interactions between coinfecting parasites may take various forms, either direct or indirect, facilitative or competitive, and may be mediated by either bottom-up or top-down mechanisms. Although each form of interaction leads to different evolutionary and ecological outcomes, it is challenging to tease them apart throughout the infection period. To establish the first step towards a mechanistic understanding of the interactions between coinfecting limited-term bacterial parasites and lifelong bacterial parasites, we studied the coinfection of Bartonella sp. (limited-term) and Mycoplasma sp. (lifelong), which commonly co-occur in wild rodents. We infected Bartonella- and Mycoplasma-free rodents with each species, and simultaneously with both, and quantified the infection dynamics and host responses. Bartonella benefited from the interaction; its infection load decreased more slowly in coinfected rodents than in rodents infected with Bartonella alone. There were no indications for bottom-up effects, but coinfected rodents experienced various changes, depending on the infection stage, in their body mass, stress levels and activity pattern, which may further affect bacterial replication and transmission. Interestingly, the infection dynamics and changes in the average coinfected rodent traits were more similar to the chronic effects of Mycoplasma infection, whereas coinfection uniquely impaired the host's physiological and behavioral stability. These results suggest that parasites with distinct life history strategies may interact, and their interaction may be asymmetric, non-additive, multifaceted and dynamic through time. Because multiple, sometimes contrasting, forms of interactions are simultaneously at play and their relative importance alternates throughout the course of infection, the overall outcome may change under different ecological conditions.

Effects of the captive and wild environment on diversity of the gut microbiome of deer mice (Peromyscus maniculatus)

Vertebrate gastrointestinal tracts have co-existed with microbes over millennia. These microbial communities provide their host with numerous benefits. However, the extent to which different environmental factors contribute to the assemblage of gut microbial communities is not fully understood. The purpose of this study was to determine how the external environment influences the development of gut microbiome communities (GMCs). Faecal samples were collected from deer mice (Peromyscus maniculatus) born and raised in captivity and the wild at approximately 3-5 weeks of age. Additional samples were collected 2 weeks later, with a subset of individuals being translocated between captive and wild environments. Microbial data were analysed using 16S rRNA next-generation Illumina HiSeq sequencing methods. GMCs of deer mice were more similar between neighbours who shared the same environment, regardless of where an individual was born, demonstrating that GMCs are significantly influenced by the surrounding environment and can rapidly change over time. Mice in natural environments contained more diverse GMCs with higher relative abundances of Ruminoccocaceae, Helicobacteraceae and Lachnospiraceae spp. Future studies should examine the fitness consequences associated with the presence/absence of microbes that are characteristic of GMCs of wild populations to gain a better understanding of environment-microbe-host evolutionary and ecological relationships.

Haemoplasmas in wild rodents: Routes of transmission and infection dynamics

The way that some parasites and pathogens persist in the hostile environment of their host for long periods remains to be resolved. Here, longitudinal field surveys were combined with laboratory experiments to investigate the routes of transmission and infection dynamics of such a pathogen-a wild rodent haemotropic bacterium, specifically a Mycoplasma haemomuris-like bacterium. Fleaborne transmission, direct rodent-to-rodent transmission and vertical transmission from fleas or rodents to their offspring were experimentally quantified, and indications were found that the main route of bacterial transmission is direct, although its rate of successful transmission is low (~20%). The bacterium's temporal dynamics was then compared in the field to that observed under a controlled infection experiment in field-infected and laboratory-infected rodents, and indications were found, under all conditions, that the bacterium reached its peak infection level after 25-45 days and then decreased to low bacterial loads, which persist for the rodent's lifetime. These findings suggest that the bacterium relies on persistency with low bacterial loads for long-term coexistence with its rodent host, having both conceptual and applied implications.

Characterization of the Skin Microbiota of the Cane Toad Rhinella cf. marina in Puerto Rico and Costa Rica

Rhinella marina is a toad native to South America that has been introduced in the Antilles, likely carrying high loads of microorganisms, potentially impacting local community diversity. The amphibian skin is involved in pathogen defense and its microbiota has been relatively well studied, however, research focusing on the cane toad microbiota is lacking. We hypothesize that the skin microbial communities will differ between toads inhabiting different geographical regions in Central America and the Caribbean. To test our hypothesis, we compared the microbiota of three populations of R. cf. marina toads, two from Costa Rican (native) and one Puerto Rican (exotic) locations. In Costa Rica, we collected 11 toads, 7 in Sarapiquí and 4 from Turrialba while in Puerto Rico, 10 animals were collected in Santa Ana. Separate swab samples were collected from the dorsal and ventral sites resulting in 42 samples. We found significant differences in the structure of the microbial communities between Puerto Rico and Costa Rica. We detected as much as 35 different phyla; however, communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Alpha diversity and richness were significantly higher in toads from Puerto Rico and betadiversity revealed significant differences between the microbiota samples from the two countries. At the genus level, we found in Santa Ana, Puerto Rico, a high dominance of Kokuria, Niabella, and Rhodobacteraceae, while in Costa Rica we found Halomonas and Pseudomonas in Sarapiquí, and Acinetobacter and Citrobacter in Turrialba. This is the first report of Niabella associated with the amphibian skin. The core microbiome represented 128 Operational Taxonomic Units (OTUs) mainly from five genera shared among all samples, which may represent the symbiotic Rhinella's skin. These results provide insights into the habitat-induced microbial changes facing this amphibian species. The differences in the microbial diversity in Puerto Rican toads compared to those in Costa Rica provide additional evidence of the geographically induced patterns in the amphibian skin microbiome, and highlight the importance of discussing the microbial tradeoffs in the colonization of new ecosystems.

Laboratory colonization stabilizes the naturally dynamic microbiome composition of field collected Dermacentor andersoni ticks

BACKGROUND

Nearly a quarter of emerging infectious diseases identified in the last century are arthropod-borne. Although ticks and insects can carry pathogenic microorganisms, non-pathogenic microbes make up the majority of their microbial communities. The majority of tick microbiome research has had a focus on discovery and description; very few studies have analyzed the ecological context and functional responses of the bacterial microbiome of ticks. The goal of this analysis was to characterize the stability of the bacterial microbiome of Dermacentor andersoni ticks between generations and two populations within a species.

METHODS

The bacterial microbiome of D. andersoni midguts and salivary glands was analyzed from populations collected at two different ecologically distinct sites by comparing field (F1) and lab-reared populations (F1-F3) over three generations. The microbiome composition of pooled and individual samples was analyzed by sequencing nearly full-length 16S rRNA gene amplicons using a Pacific Biosciences CCS platform that allows identification of bacteria to the species level.

FINDINGS

In this study, we found that the D. andersoni microbiome was distinct in different geographic populations and was tissue specific, differing between the midgut and the salivary gland, over multiple generations. Additionally, our study showed that the microbiomes of laboratory-reared populations were not necessarily representative of their respective field populations. Furthermore, we demonstrated that the microbiome of a few individual ticks does not represent the microbiome composition at the population level.

CONCLUSIONS

We demonstrated that the bacterial microbiome of D. andersoni was complex over three generations and specific to tick tissue (midgut vs. salivary glands) as well as geographic location (Burns, Oregon vs. Lake Como, Montana vs. laboratory setting). These results provide evidence that habitat of the tick population is a vital component of the complexity of the bacterial microbiome of ticks, and that the microbiome of lab colonies may not allow for comparative analyses with field populations. A broader understanding of microbiome variation will be required if we are to employ manipulation of the microbiome as a method for interfering with acquisition and transmission of tick-borne pathogens.

Distribution and Diversity of Borrelia burgdorferi Sensu Lato Group Bacteria in Sciurids of California

California has a remarkable diversity of squirrel and chipmunk species (sciurids), and five named and several unnamed genospecies in the Borrelia burgdorferi sensu lato group (BBSL) of bacteria as well, many of which utilize sciurids as reservoirs. We investigated the prevalence, spatial distribution, and diversity of BBSL in sciurids of California by literature search, PCR of 585 ear tissue samples from 15 sciurid species prospectively collected across 19 California counties, and DNA sequencing when possible. Seven publications documented BBSL infections in western gray squirrels (Sciurus griseus), fox squirrels (Sciurus niger), eastern gray squirrels (Sciurus carolinensis), Douglas squirrels (Tamiasciurus douglasii), and redwood chipmunks (Tamias ochrogenys) in northern California. Prospective sampling added new BBSL infection records for long-eared chipmunks (Tamias quadrimaculatus), Allen's chipmunks (Tamias senex), and Siskiyou chipmunks (Tamias siskiyou). Infection was detected in the Mendocino, North Coast, West Sierra, and Central Valley regions of California. The overall PCR prevalence was 9.4% (n = 585), and exceeded 40% (n = 84) in Mendocino and farther north along the Pacific coast. Redwood (40.7%, n = 81) and Siskiyou (22.2%, n = 18) chipmunks had the highest prevalence of BBSL infection. BBSL infections were associated with arboreal and semiarboreal sciurid species and species occurring in conifer forests. Western gray squirrels and Allen's chipmunks in Humboldt County and redwood chipmunks in Mendocino County were infected with B. burgdorferi sensu stricto, while we identified Borrelia bissettiae in Douglas squirrels and Siskiyou chipmunks in Humboldt and Del Norte Counties. This indicates that further study of sciurids can aid in describing the ecology of BBSL in California.

From endosymbionts to host communities: factors determining the reproductive success of arthropod vectors

Elucidating the factors determining reproductive success has challenged scientists since Darwin, but the exact pathways that shape the evolution of life history traits by connecting extrinsic (e.g., landscape structure) and intrinsic (e.g., female's age and endosymbionts) factors and reproductive success have rarely been studied. Here we collected female fleas from wild rodents in plots differing in their densities and proportions of the most dominant rodent species. We then combined path analysis and model selection approaches to explore the network of effects, ranging from micro to macroscales, determining the reproductive success of these fleas. Our results suggest that female reproductive success is directly and positively associated with their infection by Mycoplasma bacteria and their own body mass, and with the rodent species size and total density. In addition, we found evidence for indirect effects of rodent sex and rodent community diversity on female reproductive success. These results highlight the importance of exploring interrelated factors across organization scales while studying the reproductive success of wild organisms, and they have implications for the control of vector-borne diseases.

Bacterial community structure transformed after thermophilically composting human waste in Haiti

Recycling human waste for beneficial use has been practiced for millennia. Aerobic (thermophilic) composting of sewage sludge has been shown to reduce populations of opportunistically pathogenic bacteria and to inactivate both Ascaris eggs and culturable Escherichia coli in raw waste, but there is still a question about the fate of most fecal bacteria when raw material is composted directly. This study undertook a comprehensive microbial community analysis of composting material at various stages collected over 6 months at two composting facilities in Haiti. The fecal microbiota signal was monitored using a high-density DNA microarray (PhyloChip). Thermophilic composting altered the bacterial community structure of the starting material. Typical fecal bacteria classified in the following groups were present in at least half the starting material samples, yet were reduced below detection in finished compost: Prevotella and Erysipelotrichaceae (100% reduction of initial presence), Ruminococcaceae (98–99%), Lachnospiraceae (83–94%, primarily unclassified taxa remained), Escherichia and Shigella (100%). Opportunistic pathogens were reduced below the level of detection in the final product with the exception of Clostridium tetani, which could have survived in a spore state or been reintroduced late in the outdoor maturation process. Conversely, thermotolerant or thermophilic Actinomycetes and Firmicutes (e.g., Thermobifida, Bacillus, Geobacillus) typically found in compost increased substantially during the thermophilic stage. This community DNA-based assessment of the fate of human fecal microbiota during thermophilic composting will help optimize this process as a sanitation solution in areas where infrastructure and resources are limited.

Path analyses of cross-sectional and longitudinal data suggest that variability in natural communities of blood-associated parasites is derived from host characteristics and not interspecific interactions

BACKGROUND

The parasite composition of wild host individuals often impacts their behavior and physiology, and the transmission dynamics of pathogenic species thereby determines disease risk in natural communities. Yet, the determinants of parasite composition in natural communities are still obscure. In particular, three fundamental questions remain open: (1) what are the relative roles of host and environmental characteristics compared with direct interactions between parasites in determining the community composition of parasites? (2) do these determinants affect parasites belonging to the same guild and those belonging to different guilds in similar manners? and (3) can cross-sectional and longitudinal analyses work interchangeably in detecting community determinants? Our study was designed to answer these three questions in a natural community of rodents and their fleas, ticks, and two vector-borne bacteria.

METHODS

We sampled a natural population of Gerbillus andersoni rodents and their blood-associated parasites on two occasions. By combining path analysis and model selection approaches, we then explored multiple direct and indirect paths that connect (i) the environmental and host-related characteristics to the infection probability of a host by each of the four parasite species, and (ii) the infection probabilities of the four species by each other.

RESULTS

Our results suggest that the majority of paths shaping the blood-associated communities are indirect, mostly determined by host characteristics and not by interspecific interactions or environmental conditions. The exact effects of host characteristics on infection probability by a given parasite depend on its life history and on the method of sampling, in which the cross-sectional and longitudinal methods are complementary.

CONCLUSIONS

Despite the awareness of the need of ecological investigations into natural host-vector-parasite communities in light of the emergence and re-emergence of vector-borne diseases, we lack sampling methods that are both practical and reliable. Here we illustrated how comprehensive patterns can be revealed from observational data by applying path analysis and model selection approaches and combining cross-sectional and longitudinal analyses. By employing this combined approach on blood-associated parasites, we were able to distinguish between direct and indirect effects and to predict the causal relationships between host-related characteristics and the parasite composition over time and space. We concluded that direct interactions within the community play only a minor role in determining community composition relative to host characteristics and the life history of the community members.

Similarities and seasonal variations in bacterial communities from the blood of rodents and from their flea vectors

Vector-borne microbes are subject to the ecological constraints of two distinct microenvironments: that in the arthropod vector and that in the blood of its vertebrate host. Because the structure of bacterial communities in these two microenvironments may substantially affect the abundance of vector-borne microbes, it is important to understand the relationship between bacterial communities in both microenvironments and the determinants that shape them. We used pyrosequencing analyses to compare the structure of bacterial communities in Synosternus cleopatrae fleas and in the blood of their Gerbillus andersoni hosts. We also monitored the interindividual and seasonal variability in these bacterial communities by sampling the same individual wild rodents during the spring and again during the summer. We show that the bacterial communities in each sample type (blood, female flea or male flea) had a similar phylotype composition among host individuals, but exhibited seasonal variability that was not directly associated with host characteristics. The structure of bacterial communities in male fleas and in the blood of their rodent hosts was remarkably similar and was dominated by flea-borne Bartonella and Mycoplasma phylotypes. A lower abundance of flea-borne bacteria and the presence of Wolbachia phylotypes distinguished bacterial communities in female fleas from those in male fleas and in rodent blood. These results suggest that the overall abundance of a certain vector-borne microbe is more likely to be determined by the abundance of endosymbiotic bacteria in the vector, abundance of other vector-borne microbes co-occurring in the vector and in the host blood and by seasonal changes, than by host characteristics.