Microbial Ecology

Biological soil crust (biocrust) is a composite of mosses, lichens, and bacteria that performs many important soil system functions, including increasing soil stability, protecting against wind erosion, reducing nutrient loss, and mediating carbon and nitrogen fixation cycles. These cold desert and steppe ecosystems are expected to experience directional changes in both climate and disturbance. These include increased temperatures, precipitation phase changes, and increased disturbance from anthropogenic land use. In this study, we assessed how climate and grazing disturbance may affect the abundance and diversity of bacteria in biocrusts in cold steppe ecosystems located in southwestern Idaho, USA. To our knowledge, our study is the first to document how biocrust bacterial composition and diversity change along a cold steppe climatic gradient. Analyses based on 16S small subunit ribosomal RNA gene sequences identified the phylum Actinobacteria as the major bacterial component within study site biocrusts (relative abundance = 36–51%). The abundance of the phyla Actinobacteria and Firmicutes was higher at elevations experiencing cooler, wetter climates, while the abundance of Cyanobacteria, Proteobacteria, and Chloroflexi decreased. The abundance of the phyla Cyanobacteria and Proteobacteria showed no significant evidence of decline in grazed areas. Taken together, results from this study indicate that bacterial communities from rolling biocrusts found in cold steppe ecosystems are affected by climate regime and differ substantially from other cold desert ecosystems, resulting in potential differences in nutrient cycling and ecosystem dynamics.

Almost all living plants can be simultaneously colonised by arbuscular mycorrhizal fungi in the roots and endophytes in the shoots, while also being attacked by insect herbivores. However, to date, no study has ever examined the multitrophic interactions between these two different fungal groups and insects on any species of forb. Here, we examined the effects of two commercial species mixtures of arbuscular mycorrhizal fungi (AMF) and two foliar endophytes (Colletotrichum acutatum and Cladosporium oxysporum) on the growth of an invasive weed, Impatiens glandulifera, and the aphids that attack it. AMF reduced plant biomass, which was most evident when C. oxysporum was inoculated. Mycorrhizal fungi had few effects on aphids, and these depended on the identity of the endophytes present. Meanwhile, endophytes tended to increase aphid numbers, but this depended on the identity of the AMF inoculum. Throughout, there were differences in the responses of the plant to the two mycorrhizal mixtures, demonstrating clear AMF specificity in this plant. These specific effects were also strongly affected by the endophytes, with a greater number of interactions found between the AMF and endophytes than between the endophytes themselves. In particular, AMF reduced infection levels by the endophytes, while some endophyte inoculations reduced mycorrhizal colonisation. We suggest that both AMF and endophytes could play an important part in future biological control programmes of weeds, but further multitrophic experiments are required to unravel the complexity of interactions between spatially separated parts of the plant microbiome.

Honeybees are important pollinators, having an essential role in the ecology of natural and agricultural environments. Honeybee colony losses episodes reported worldwide and have been associated with different pests and pathogens, pesticide exposure, and nutritional stress. This nutritional stress is related to the increase in monoculture areas which leads to a reduction of pollen availability and diversity. In this study, we examined whether nutritional stress affects honeybee gut microbiota, bee immunity, and infection by Nosema ceranae, under laboratory conditions. Consumption of Eucalyptus grandis pollen was used as a nutritionally poor-quality diet to study nutritional stress, in contraposition to the consumption of polyfloral pollen. Honeybees feed with Eucalyptus grandis pollen showed a lower abundance of Lactobacillus mellifer and Lactobacillus apis (Firm-4 and Firm-5, respectively) and Bifidobacterium spp. and a higher abundance of Bartonella apis, than honeybees fed with polyfloral pollen. Besides the impact of nutritional stress on honeybee microbiota, it also decreased the expression levels of vitellogenin and genes associated to immunity (glucose oxidase, hymenoptaecin and lysozyme). Finally, Eucalyptus grandis pollen favored the multiplication of Nosema ceranae. These results show that nutritional stress impacts the honeybee gut microbiota, having consequences on honeybee immunity and pathogen development. Those results may be useful to understand the influence of modern agriculture on honeybee health.

Understanding the distribution of bacteria is a major goal of microbial ecology which remains to be fully deciphered. In this study, a model 50 °C temperature gradient at a Northern Thailand hot spring was analyzed to determine how the bacterial communities were structured in the environment. Communities were examined through 16S rRNA gene amplification, denaturing gradient gel electrophoresis, and sequencing. The two major phyla, Cyanobacteria and Chloroflexi, showed characteristic distributions along the temperature gradient. Different clades were allocated at specific portions of the gradient. Comparisons of the bacterial communities along the temperature gradient showed sharp decreases of similarity at increasing temperature difference. Peaks of maximum richness were observed at 50 and 70 °C. This study contributes to explain how environmental conditions and microbial interactions can influence the distribution of specific bacterial clades and phyla shaping the structure of microbial communities in nature.

The Salt Plains National Wildlife Refuge (SPNWR) near Cherokee, Oklahoma, contains a barren salt flat where Permian brine rises to the surface and evaporates under dry conditions to leave a crust of white salt. Rainfall events dissolve the salt crust and create ephemeral streams and ponds. The rapidly changing salinity and high surface temperatures, salinity, and UV exposure make this an extreme environment. The Salt Plains Microbial Observatory (SPMO) examined the soil microbial community of this habitat using classic enrichment and isolation techniques and phylogenetic rDNA studies. Rich growth media have been emphasized that differ in total salt concentration and composition. Aerobic heterotrophic enrichments were performed under a variety of conditions. Heterotrophic enrichments and dilution plates have generated 105 bacterial isolates, representing 46 phylotypes. The bacterial isolates have been characterized phenotypically and subjected to rDNA sequencing and phylogenetic analyses. Fast-growing isolates obtained from enrichments with 10% salt are predominantly from the gamma subgroup of the Proteobacteria and from the low GC Gram-positive cluster. Several different areas on the salt flats have yielded a variety of isolates from the Gram-negative genera Halomonas, Idiomarina, Salinivibrio, and Bacteroidetes. Gram-positive bacteria are well represented in the culture collection including members of the Bacillus, Salibacillus, Oceanobacillus, and Halobacillus.

The incorporation of [3H-methyl] thymidine (3H-TdR) by Eubacteria, bacterial groups (α- and β-Proteobacteria, Cytophaga–Flavobacter), and Archaea was measured according to temperature (7 and 17°C) and nutrient levels (nitrogen, phosphorus, and carbon) in a lacustrine system (Sep, France). Short-term incubation was performed using a combination of microautoradiography and fluorescent in situ hybridization. Irrespective of the temperatures and nutrients studied, all the major phylogenetic bacterial groups assimilated 3H-TdR, and in most of the treatments studied, the proportion of β-Proteobacteria taking up 3H-TdR was higher than those in the other bacterial groups. The proportion of Bacteria and different bacterial groups studied incorporating 3H-TdR were significantly increased, approximately 1.5-fold, by temperature except for α-Proteobacteria (7.6-fold). The nutrient effect was not the same for the different bacterial groups according to the temperatures studied. The proportions of α-Proteobacteria (at both temperatures) and Cytophaga–Flavobacter (at 7°C) taking up 3H-TdR were significantly decreased and increased by adding N and P, respectively. Also, adding N, P, and C increased and decreased the percentage of β-Proteobacteria incorporating 3H-TdR at 7 and 17°C, respectively. The archaeal community showed a similar proportion of active cells (i.e., 3H-TdR) to the bacterial community, and uptake of 3H-TdR by Archaea was significantly increased (P < 0.05) by both temperature and nutrients. Thus, the assimilation of 3H-TdR by bacterial groups and Archaea in lacustrine system is significantly controlled by both temperature and nutrients.

To understand how microbiota influence plant populations in nature, it is important to examine the biogeographic distribution of plant-associated microbiomes and the underlying mechanisms. However, we currently lack a fundamental understanding of the biogeography of plant microbiomes across populations and the environmental and host genetic factors that shape their distribution. Leveraging the broad distribution and extensive genetic variation in duckweeds (the Lemna species complex), we identified key factors that governed plant microbiome diversity and compositional variation geographically. In line with the microbial biogeography of free-living microbiomes, we observed higher bacterial richness in temperate regions relative to lower latitudes in duckweed microbiomes (with 10% higher in temperate populations). Our analyses revealed that higher temperature and sodium concentration in aquatic environments showed a negative impact on duckweed bacterial richness, whereas temperature, precipitation, pH, and concentrations of phosphorus and calcium, along with duckweed genetic variation, influenced the biogeographic variation of duckweed bacterial community composition. Analyses of plant microbiome assembly processes further revealed that niche-based selection played an important role (26%) in driving the biogeographic variation of duckweed bacterial communities, alongside the contributions of dispersal limitation (33%) and drift (39%). These findings add significantly to our understanding of host-associated microbial biogeography and provide important insights for predicting plant microbiome vulnerability and resilience under changing climates and intensifying anthropogenic activities.

Toxin production is an adaptation that allows cyanobacteria in resource-limiting environments to ameliorate the effects of herbivory and competition with other phototrophs. We demonstrate that the cyanobacterial toxins anatoxin-a and microcystin-LR paralyze the motile green alga Chlamydomonas reinhardtii. In addition, both purified toxins and cyanobacterial extracellular products containing these toxins cause the alga to settle faster than in nontoxic media. In microcosm experiments, the presence of either the cyanobacterium or its extracellular products induce settling in the alga, similar to the response observed with the addition of both anatoxin-a and microcystin-LR. The cyanobacterial production of paralyzing toxins represents a novel mechanism for phytoplankton settling. This prokaryotic/eukaryotic chemical interaction may create a competitor-free zone for cyanobacteria in lake environments, predicating optimal conditions for a toxic cyanobacterial bloom.

The research field of animal and plant symbioses is advancing from studying interactions between two species to whole communities of associates. High-throughput sequencing of microbial communities supports multiplexed sampling for statistically robust tests of hypotheses about symbiotic associations. We focus on ambrosia beetles, the increasingly damaging insects primarily associated with fungal symbionts, which have also been reported to support bacteria. To analyze the diversity, composition, and specificity of the beetles’ prokaryotic associates, we combine global sampling, insect anatomy, 454 sequencing of bacterial rDNA, and multivariate statistics to analyze prokaryotic communities in ambrosia beetle mycangia, organs mostly known for transporting symbiotic fungi. We analyze six beetle species that represent three types of mycangia and include several globally distributed species, some with major economic importance (Dendroctonus frontalis, Xyleborus affinis, Xyleborus bispinatus–ferrugineus, Xyleborus glabratus, Xylosandrus crassiusculus, and Xylosandrus germanus). Ninety-six beetle mycangia yielded 1,546 bacterial phylotypes. Several phylotypes appear to form the core microbiome of the mycangium. Three Mycoplasma (originally thought restricted to vertebrates), two Burkholderiales, and two Pseudomonadales are repeatedly present worldwide in multiple beetle species. However, no bacterial phylotypes were universally present, suggesting that ambrosia beetles are not obligately dependent on bacterial symbionts. The composition of bacterial communities is structured by the host beetle species more than by the locality of origin, which suggests that more bacteria are vertically transmitted than acquired from the environment. The invasive X. glabratus and the globally distributed X. crassiusculus have unique sets of bacteria, different from species native to North America. We conclude that the mycangium hosts in multiple vertically transmitted bacteria such as Mycoplasma, most of which are likely facultative commensals or parasites.