Geology Reports⌕ Search

SEARCH · Geology Reports

Results for “Microbiome”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3Linked to original sources
USGS2026

Functional restructuring of the global soil microbiome under multiple stressors

Microbes, as the planet’s most abundant and diverse organisms, drive soil functions globally and are vulnerable to environmental stressors triggered by global change. Yet, knowledge regarding the impacts of multiple environmental stressors on their functional profiles as well as the consequences for soil functionality largely remains unknown. Here, we analyze two global-scale datasets including information on soil metagenomics and multiple environmental stressors. We find that across terrestrial ecosystems worldwide, up to 60% of all functional genes significantly shift when soil microbes experience the high-level of concurrent stressors. In this regard, the relative abundances of genes involved in microbial growth are negatively linked to the increasing number of stressors. Conversely, those genes linked to stress resistance and energy production exhibit positive responses. Taken together, our findings highlight a significant restructuring of global soil functional microbiomes in response to multiple environmental stressors. Consequently, such restructuring drives community-level shifts in matter and energy reallocations, thereby impacting the maintenance of soil functionality under the projected global change.

Nature Communications↗
USGS2023

A meta-analysis of the stony coral tissue loss disease microbiome finds key bacteria in unaffected and lesion tissue in diseased colonies

Stony coral tissue loss disease (SCTLD) has been causing significant whole colony mortality on reefs in Florida and the Caribbean. The cause of SCTLD remains unknown, with the limited concurrence of SCTLD-associated bacteria among studies. We conducted a meta-analysis of 16S ribosomal RNA gene datasets generated by 16 field and laboratory SCTLD studies to find consistent bacteria associated with SCTLD across disease zones (vulnerable, endemic, and epidemic), coral species, coral compartments (mucus, tissue, and skeleton), and colony health states (apparently healthy colony tissue (AH), and unaffected (DU) and lesion (DL) tissue from diseased colonies). We also evaluated bacteria in seawater and sediment, which may be sources of SCTLD transmission. Although AH colonies in endemic and epidemic zones harbor bacteria associated with SCTLD lesions, and aquaria and field samples had distinct microbial compositions, there were still clear differences in the microbial composition among AH, DU, and DL in the combined dataset. Alpha-diversity between AH and DL was not different; however, DU showed increased alpha-diversity compared to AH, indicating that, prior to lesion formation, corals may undergo a disturbance to the microbiome. This disturbance may be driven by Flavobacteriales, which were especially enriched in DU. In DL, Rhodobacterales and Peptostreptococcales–Tissierellales were prominent in structuring microbial interactions. We also predict an enrichment of an alpha-toxin in DL samples which is typically found in Clostridia. We provide a consensus of SCTLD-associated bacteria prior to and during lesion formation and identify how these taxa vary across studies, coral species, coral compartments, seawater, and sediment.

ISME Communications↗
USGS2023

Fecal DNA metabarcoding shows credible short-term prey detections and explains variation in the gut microbiome of two polar bear subpopulations

This study developed and evaluated DNA metabarcoding to identify the presence of pinniped and cetacean prey DNA in fecal samples of East Greenland (EG) and Southern Beaufort Sea (SB) polar bears Ursus maritimus sampled in the spring of 2015-2019. Prey DNA was detected in half (49/92) of all samples, and when detected, ringed seal Pusa hispida was the predominant prey species, identified in 100% (22/22) of EG and 81% (22/27) of SB polar bear samples with prey DNA detected. Bearded seal Erignathus barbatus DNA was found in 19% (5/27) of SB polar bear samples for which prey DNA was detected. Prey DNA detection frequencies and relative abundances were compared to estimates from quantitative fatty acid signature analysis (QFASA) for a subset of SB polar bears. Ringed seal and bearded seal were the main prey identified by both methods, but QFASA also identified 2 cetacean prey species not found by prey DNA. Differences in DNA metabarcoding vs. QFASA results were likely related to the different dietary timescales captured by each approach, i.e. short-term vs. long-term diet, respectively. Prey DNA detection, sex/age class, and subpopulation significantly explained variation in polar bear gut bacterial composition. Polar bear samples with prey DNA detected were associated with higher abundances of the bacterial classes Clostridia and Bacilli and lower abundances of Negativicutes. Fecal DNA metabarcoding is thus useful for identifying recent prey of polar bears, complementing quantitative and likely longer-term QFASA estimates, and may help understand variation in the polar bear gut microbiome.

Marine Ecology Progress Series (MEPS)↗
USGS2017

Biogeographic comparison of Lophelia -associated bacterial communities in the Western Atlantic reveals conserved core microbiome

Over the last decade, publications on deep-sea corals have tripled. Most attention has been paid to Lophelia pertusa , a globally distributed scleractinian coral that creates critical three-dimensional habitat in the deep ocean. The bacterial community associated with L. pertusa has been previously described by a number of studies at sites in the Mediterranean Sea, Norwegian fjords, off Great Britain, and in the Gulf of Mexico (GOM). However, use of different methodologies prevents direct comparisons in most cases. Our objectives were to address intra-regional variation and to identify any conserved bacterial core community. We collected samples from three distinct colonies of L. pertusa at each of four locations within the western Atlantic: three sites within the GOM and one off the east coast of the United States. Amplicon libraries of 16S rRNA genes were generated using primers targeting the V4–V5 hypervariable region and 454 pyrosequencing. The dominant phylum was Proteobacteria (75–96%). At the family level, 80–95% of each sample was comprised of five groups: Pirellulaceae, Pseudonocardiaceae, Rhodobacteraceae, Sphingomonadaceae, and unclassified Oceanospirillales. Principal coordinate analysis based on weighted UniFrac distances showed a clear distinction between the GOM and Atlantic samples. Interestingly, the replicate samples from each location did not always cluster together, indicating there is not a strong site-specific influence. The core bacterial community, conserved in 100% of the samples, was dominated by the operational taxonomic units of genera Novosphingobium and Pseudonocardia , both known degraders of aromatic hydrocarbons. The sequence of another core member, Propionibacterium , was also found in prior studies of L. pertusa from Norway and Great Britain, suggesting a role as a conserved symbiont. By examining more than 40,000 sequences per sample, we found that GOM samples were dominated by the identified conserved core sequences, whereas open Atlantic samples had a much higher proportion of locally consistent bacteria. Further, predictive functional profiling highlights the potential for the L. pertusa microbiome to contribute to chemoautotrophy, nutrient cycling, and antibiotic production.

Florida↗
USGS2026

Core microbiomes as a potential fingerprinting method of Western USA dust sources

Introduction: Changing frequency and intensity of dust emissions impacts ecosystems and human health. Dust carries microbes, nutrients, heavy metals, and other materials that may change environmental biogeochemistry at deposition sites. Identifying dust sources provides key information on where and when mitigation strategies should be employed. However, commonly used geochemical or isotopic tracers are often not capable of distinguishing between geographic regions. Methods: We explored whether soil bacterial communities may provide distinct fingerprints of dust sources in the western United States. We identified bacterial core communities of dust from ten locations monitored by the National Wind Erosion Research Network (NWERN) with varied land use (cropland, rangeland, and playa), and compared communities to location, soil, and regional characteristics. Samples were collected monthly from Modified Wilson and Cooke (MWAC) samplers, composited by season (spring, summer, and fall), and analyzed using 16S rRNA sequencing. Results: We found distinct bacterial core communities that reflected dust source characteristics. In order of importance, precipitation levels ( p = 0.0001), location ( p = 0.0001), soil texture ( p = 0.0001), seasonality ( p = 0.0001), and elevation (p = 0.0002) were correlated with bacterial community composition. Discussion: Distinct bacterial core communities were associated with site characteristics such as biocrusts, playas, and military base proximity. Our results suggest that the use of core microbiomes may offer a fingerprinting method to identify dust source regions.

Colorado, Nevada, New Mexico, North Dakota, Oklaho↗
USGS2025

A short-term sublethal oral exposure to microcystin-LR disrupts cecal microbiome homeostasis in mallard

Introduction: The frequency of cyanobacterial blooms seems to have increased globally in recent decades due to human induced eutrophication and climate change. Cyanobacterial blooms can produce several groups of toxins, among which microcystin-LR (MC-LR) is one of the most abundant. Effects of MC-LR on avian microbiome have not been studied and studies in laboratory murines have been limited to metabarcoding of prokaryotes. Methods: Using RNA shotgun sequencing, we compared the richness and composition of metabolically active prokaryotes, expressed virulence factors, antimicrobial resistance genes, metabolic pathways, Gene Ontology terms, enzymes, and proteins in mallards (Anas platyrhynchos) that were orally exposed to a sublethal dose of MC-LR for one week and unexposed birds. Results: Richness and composition of all compared features did not differ between exposed and control birds and none were differentially expressed between exposure groups. However, richness and/or composition of all features except virulence factors and Carbohydrate Active enzymes had multiple-fold greater dispersion in exposed birds than in controls. This effect was especially pronounced in expressed metabolic (MetaCyc) pathways. Discussion: Our results suggest that MC-LR exposure had a stochastic (rather than deterministic) effect on cecal microbiota, especially its function. Observed disturbance of the microbiota homeostasis is consistent with the Anna Karenina Principle. This principle has been documented in a wide range of eukaryotes using primarily microbial community metabarcoding. Although stochastic disturbance of microbiota function has been hypothesized, our study seems to be the first to demonstrate this in an experimental study.

Wisconsin↗
USGS2026

Is "weediness" and "invasiveness" of weeds a function of the plant microbiome?

Over the past several decades, the extent to which microbes enhance plant development and health has become clearer; however, this has not been explored in terms of the aggressiveness and hardiness of weedy plants. In this review, we explore the hypothesis that many features of weeds and invasive plants are related to the activities of plant microbiomes. Microbes contribute to weed growth, fecundity, and fitness. They also play roles in soils, and in plants as endophytes, where they modulate plant development and protect the host from pathogens, insects, animals, and abiotic stresses. In addition, the adaptability and hardiness of weeds partly stem from the effects of endophytes on plant gene expression and genetic diversity. Weed control often involves multiple applications of herbicides or other treatments that can be costly and destructive. Weed and invasive plant control for agriculture and environment goes beyond monetary costs to negative impacts on people, animals and environment. However, with a more complete knowledge of the roles played by microbes, their symbiotic interactions may be altered to diminish aggressive traits less expensively and with fewer non target effects on environmental, human and animal health.

Grass Research↗
USGS2021

Novel microbiome dominated by Arcobacter during anoxic excurrent flow from an ocean blue hole in Andros Island, The Bahamas

Andros Island, The Bahamas, composed of porous carbonate rock, has about 175 inland blue holes and over 50 known submerged ocean caves along its eastern barrier reef. These ocean blue holes can have both vertical and horizontal zones that penetrate under the island. Tidal forces drive water flow in and out of these caves. King Kong Cavern has a vertical collapse zone and a deep penetration under Andros Island that emits sulfidic, anoxic water and masses of thin, mucoid filaments ranging to meters in length and off-white turbid water during ebb flow. Our objective was to determine the microbial composition of this mucoid material and the unconsolidated water column turbidity based on the concept that they represent unique lithoautotrophic microbial material swept from the cave into the surrounding ocean. Bacterial DNA extracted from these filaments and surrounding turbid water was characterized using PCR that targeted a portion of the 16S rRNA gene. The genus Arcobacter dominated both the filaments and the water column above the cave entrance. Arcobacter nitrofigilis and Arcobacter sp. UDC415 in the mucoid filaments accounted for as much as 80% of mapped DNA reads. In the water column Arcobacter comprised from 65% to over 85% of the reads in the depth region from about 18 m to 34 m. Bacterial species diversity was much higher in surface water and in water deeper than 36 m than in the intermediate zone. Community composition indicates that ebb flow from the cavern influences the entire water column at least to within 6 m of the surface and perhaps the near surface as well.

Andros Island, King Kong Cavern↗
USGS2024

Ticks without borders: Microbiome of immature neotropical tick species parasitizing migratory songbirds along northern Gulf of Mexico

Introduction: The long-distance, seasonal migrations of birds make them an effective ecological bridge for the movement of ticks. The introduction of exotic tick species to new geographical regions can cause the emergence of novel tick-borne pathogens. This study examined the prevalence of exotic tick species parasitizing migratory songbirds at stopover sites along the northern Gulf of Mexico using the mitochondrial 12S rRNA gene. Methods: Overall, 421 individual ticks in the genera Amblyomma , Haemaphysalis , and Ixodes were recorded from 28 songbird species, of which Amblyomma and Amblyomma longirostre were the most abundant tick genera and species, respectively. A high throughput 16S ribosomal RNA sequencing approach characterized the microbial communities and identified pathogenic microbes in all tick samples. Results and discussion: Microbial profiles showed that Proteobacteria was the most abundant phylum. The most abundant pathogens were Rickettsia and endosymbiont Francisella , Candidatus Midichloria , and Spiroplasma . Permutation multivariate analysis of variance revealed that the relative abundance of Francisella and Rickettsia drives microbial patterns across the tick genera. We also noted a higher percentage of positive correlations in microbe-microbe interactions among members of the microbial communities. Network analysis suggested a negative correlation between a) Francisella and Rickettsia and, b) Francisella and Cutibacterium . Lastly, mapping the distributions of bird species parasitized during spring migrations highlighted geographic hotspots where migratory songbirds could disperse ticks and their pathogens at stopover sites or upon arrival to their breeding grounds, the latter showing mean dispersal distances from 421–5003 kilometers. These findings spotlight the potential role of migratory birds in the epidemiology of tick-borne pathogens.

Alabama, Louisiana↗
USGS2023

Energy-related wastewater contamination alters microbial communities of sediment, water, and amphibian skin

To inform responsible energy development, it is important to understand the ecological effects of contamination events. Wastewaters, a common byproduct of oil and gas extraction, often contain high concentrations of sodium chloride (NaCl) and heavy metals (e.g., strontium and vanadium). These constituents can negatively affect aquatic organisms, but there is scarce information for how wastewaters influence potentially distinct microbiomes in wetland ecosystems . Additionally, few studies have concomitantly investigated effects of wastewaters on the habitat (water and sediment) and skin microbiomes of amphibians or relationships among these microbial communities. We sampled microbiomes of water, sediment, and skin of four larval amphibian species across a gradient of chloride contamination (0.04–17,500 mg/L Cl) in the Prairie Pothole Region of North America. We detected 3129 genetic phylotypes and 68 % of those phylotypes were shared among the three sample types. The most common shared phylotypes were Proteobacteria, Firmicutes, and Bacteroidetes. Salinity of wastewaters increased dissimilarity within all three microbial communities, but not the diversity or richness of water and skin microbial communities. Strontium was associated with lower diversity and richness of sediment microbial communities, but not those of water or amphibian skin, likely because metal deposition occurs in sediment when wetlands dry. Based on Bray Curtis distance matrices, sediment microbiomes were similar to those of water, but neither had substantial overlap with amphibian microbiomes. Species identity was the strongest predictor of amphibian microbiomes; frog microbiomes were similar but differed from that of the salamander, whose microbiome had the lowest richness and diversity. Understanding how effects of wastewaters on the dissimilarity, richness, and diversity of microbial communities also influence the ecosystem function of communities will be an important next step. However, our study provides novel insight into the characteristics of, and associations among, different wetland microbial communities and effects of wastewaters from energy production.

Montana, North Dakota↗
USGS2021

Effects of supplemental feeding on the fecal bacterial communities of Rocky Mountain elk in the Greater Yellowstone Ecosystem

Supplemental feeding of wildlife is a common practice often undertaken for recreational or management purposes, but it may have unintended consequences for animal health. Understanding cryptic effects of diet supplementation on the gut microbiomes of wild mammals is important to inform conservation and management strategies. Multiple laboratory studies have demonstrated the importance of the gut microbiome for extracting and synthesizing nutrients, modulating host immunity, and many other vital host functions, but these relationships can be disrupted by dietary perturbation. The well-described interplay between diet, the microbiome, and host health in laboratory and human systems highlights the need to understand the consequences of supplemental feeding on the microbiomes of free-ranging animal populations. This study describes changes to the gut microbiomes of wild elk under different supplemental feeding regimes. We demonstrated significant cross-sectional variation between elk at different feeding locations and identified several relatively low-abundance bacterial genera that differed between fed versus unfed groups. In addition, we followed four of these populations through mid-season changes in supplemental feeding regimes and demonstrated a significant shift in microbiome composition in a single population that changed from natural forage to supplementation with alfalfa pellets. Some of the taxonomic shifts in this population mirrored changes associated with ruminal acidosis in domestic livestock. We discerned no significant changes in the population that shifted from natural forage to hay supplementation, or in the populations that changed from one type of hay to another. Our results suggest that supplementation with alfalfa pellets alters the native gut microbiome of elk, with potential implications for population health.

Wyoming↗
USGS2021

Unexpected diversity of Endozoicomonas in deep-sea corals

ABSTRACT: The deep ocean hosts a large diversity of azooxanthellate cold-water corals whose associated microbiomes remain to be described. While the bacterial genus Endozoicomonas has been widely identified as a dominant associate of tropical and temperate corals, it has rarely been detected in deep-sea corals. Determining microbial baselines for these cold-water corals is a critical first step to understanding the ecosystem services their microbiomes contribute, while providing a benchmark against which to measure responses to environmental change or anthropogenic effects. Samples of Acanthogorgia aspera , A. spissa , Desmophyllum dianthus , and D. pertusum ( Lophelia pertusa ) were collected from western Atlantic sites off the US east coast and from the northeastern Gulf of Mexico. Microbiomes were characterized by 16S rRNA gene amplicon surveys. Although D. dianthus and D. pertusum have recently been combined into a single genus due to their genetic similarity, their microbiomes were significantly different. The Acanthogorgia spp. were collected from submarine canyons in different regions, but their microbiomes were extremely similar and dominated by Endozoicomonas . This is the first report of coral microbiomes dominated by Endozoicomonas occurring below 1000 m, at temperatures near 4°C. D. pertusum from 2 Atlantic sites were also dominated by distinct Endozoicomonas , unlike D. pertusum from other sites described in previous studies, including the Gulf of Mexico, the Mediterranean Sea and a Norwegian fjord.

Marine Ecology Progress Series↗
USGS2019

Microbial associations of four species of algal symbiont-bearing Foraminifers from the Florida Reef Tract, USA

While microbiome research is a rapidly expanding field of study, relatively little is known of the microbiomes associated with Foraminifera. This preliminary study investigated microbes associated with four species of Foraminifera, representing two taxonomic orders, which host three kinds of algal endosymbionts. A major objective was to explore potential influences on the microbiome composition, including phylogenetic relatedness among the host species, similarities in algal symbionts hosted, and environmental conditions from which the specimens were collected. Samples examined from two locations along the middle Florida Keys reef tract included 45 foraminiferal specimens and four environmental samples. Bacterial DNA extraction from individual specimens was followed by amplification and amplicon sequencing of the V4 variable region of the 16S rRNA gene; results were obtained from 21 specimens. The Order Miliolida, Family Soritidae, was represented by 5–8 specimens of each of three species: Archaias angulatus and Cyclorbiculina compressa , which both host chlorophyte symbionts, and Sorites orbiculus , which hosts dinoflagellate symbionts. Three Ar. angulatus specimens from which the microbiome was successfully sequenced shared 177 OTUs. Six C. compressa specimens successfully sequenced shared 58 OTUs, of which 31 were also shared by the three specimens of Ar. angulatus . Four successfully sequenced S. orbiculus specimens shared 717 unique OTUs. The 13 soritid specimens shared 26 OTUs, 23 of which represented Proteobacteria, predominantly of the bacterial family Rhodobacteraceae. The fourth foraminiferal species, Amphistegina gibbosa (Order Rotaliida) hosts diatom endosymbionts. Bacterial DNA extraction was attempted on 16 Am. gibbosa , including both normal-appearing and partly-bleached specimens. Only six OTUs, four of which represented Proteobacteria, were found in all eight specimens successfully sequenced. The partly bleached specimens shared nearly twice as many unique microbial OTUs (32) as the normal-appearing specimens (19). All Am. gibbosa specimens shared only four microbial OTUs with the soritid species, three of which may have been contaminants, indicating minimal commonality between the microbiomes of Am. gibbosa and the soritid taxa.

Florida↗
USGS2023

Functional gene composition and metabolic potential of deep-sea coral-associated microbial communities

Over the past decade, an abundance of 16S rRNA gene surveys have provided microbiologists with data regarding the prokaryotes present in a coral-associated microbial community. Functional gene studies that provide information regarding what those microbes might do are fewer, particularly for non-tropical corals. Using the GeoChip 5.0S microarray, we present a functional gene study of microbiomes from five species of cold-water corals collected from depths of 296–1567 m. These species included two octocorals, Acanthogorgia aspera and Acanthogorgia spissa , and three stony corals: Desmophyllum dianthus , Desmophyllum pertusum (formerly Lophelia pertusa ), and Enallopsammia profunda . A total of 24,281 gene sequences (representing different microbial taxa) encoding for 383 functional gene families and representing 9 metabolic gene categories were identified. Gene categories included metabolism of carbon, nitrogen, phosphorus, and sulfur, as well as virulence, organic remediation, metal homeostasis, secondary metabolism and phylogeny. We found that microbiomes from Acanthogorgia spp. were the most functionally distinct but also least diverse compared against those from stony corals. Desmophyllum spp. microbiomes were more similar to each other than to E. profunda . Of 383 total gene families detected in this study, less than 20% were significantly different among these deep-water coral species. Similarly, out of 59 metabolic sub-categories for which we were able to make a direct comparison to microbiomes of tropical corals, only 7 were notably different: anaerobic ammonium oxidation (anammox), chitin degradation, and dimethylsulfoniopropionate (DMSP) degradation, all of which had higher representations in deep-water corals; and chromium homeostasis/resistance, copper homeostasis/resistance, antibiotic resistance, and methanogenesis, all of which had higher representation in tropical corals. This implies a broad-scale convergence of the microbial functional genes present within the coral holobiont, independent of coral species, depth, symbiont status, and morphology.

Coral Reefs↗
USGS2025

Comparing contaminants of emerging concern and microbial signatures of wastewater treated by membrane bioreactor and oxidation ditch methods

Membrane bioreactors (MBRs) are an attractive option for upgrades to aging wastewater treatment infrastructure across the United States (U.S.) because they have a relatively small footprint and can handle various wastewater loading conditions. However, little is known regarding the efficiency with which MBRs can reduce contaminants of emerging concern (CECs) and microbial loads, or how they influence the microbiome of wastewater effluent. In 2022, we collected nine paired samples of primary treated effluent (PRI), secondary effluent treated by oxidation ditches (OXI), and secondary effluent treated by MBR from a facility in Minnesota, U.S. Samples were analyzed for CECs including 4 alkylphenol ethoxylates, 6 bisphenol analogues, 20 hormones, 110 pharmaceuticals, and 82 pesticides as well as heterotrophic bacteria counts (HPC) and microbiome communities. Except for pesticides, total sample concentrations of CEC classes in OXI and MBR effluents were similar and lower compared to PRI ( p < 0.01). Pesticide concentrations were similar among all treatments. HPC was lower in MBR, compared to OXI, in 67% of samples. Despite limited differences in CEC signatures, differences in the microbiome between the two secondary treatments were observed. OXI showed more distinct differences in bacterial operational taxonomic unit (OTU) presence from PRI, compared to MBR. Relations between some contaminant groups ( e.g. , pharmaceuticals, bisphenols) and effluent microbiomes were observed, though most correlated with PRI effluent. Results from our study indicate that MBR is as effective as OXI at producing high-quality effluent and offers a viable alternative to conventional secondary treatment methods. This full-scale study provides data that helps fill knowledge gaps related to MBR performance outside of lab or benchtop experiments and direct comparison to OXI treatment.

Environmental Science: Water Research & Technology↗
USGS2019

Is there convergence of gut microbes in blood-feeding vertebrates?

Animal microbiomes play an important role in dietary adaptation, yet the extent to which microbiome changes exhibit parallel evolution is unclear. Of particular interest is an adaptation to extreme diets, such as blood, which poses special challenges in its content of proteins and lack of essential nutrients. In this study, we assessed taxonomic signatures (by 16S rRNA amplicon profiling) and potential functional signatures (inferred by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt)) of haematophagy in birds and bats. Our goal was to test three alternative hypotheses: no convergence of microbiomes, convergence in taxonomy and convergence in function. We find a statistically significant effect of haematophagy in terms of microbial taxonomic convergence across the blood-feeding bats and birds, although this effect is small compared to the differences found between haematophagous and non-haematophagous species within the two host clades. We also find some evidence of convergence at the predicted functional level, although it is possible that the lack of metagenomic data and the poor representation of microbial lineages adapted to haematophagy in genome databases limit the power of this approach. The results provide a paradigm for exploring convergent microbiome evolution replicated with independent contrasts in different host lineages.

Philosophical Transactions of the Royal Society B:↗
USGS2020

Differences in rhizosphere microbial communities between native and non‐native Phragmites australis may depend on stand density

Microorganisms surrounding plant roots may benefit invasive species through enhanced mutualism or decreased antagonism, when compared to surrounding native species. We surveyed the rhizosphere soil microbiome of a prominent invasive plant, Phragmites australis , and its co‐occurring native subspecies for evidence of microbial drivers of invasiveness. If the rhizosphere microbial community is important in driving plant invasions, we hypothesized that non‐native Phragmites would cultivate a different microbiome from native Phragmites , containing fewer pathogens, more mutualists, or both. We surveyed populations of native and non‐native Phragmites across Michigan and Ohio USA, and we described rhizosphere microbial communities using culture‐independent next‐generation sequencing. We found little evidence that native and non‐native Phragmites cultivate distinct bacterial, fungal, or oomycete rhizosphere communities. Microbial community differences in our Michigan survey were not associated with plant lineage but were mainly driven by environmental factors, such as soil saturation and nutrient concentrations. Intensive sampling along transects consisting of dense monocultures of each lineage and mixed zones revealed bacterial community differences between lineages in dense monoculture, but not in mixture. We found no evidence of functional differences in the microbial communities surrounding each lineage. We extrapolate that the invasiveness of non‐native Phragmites , when compared to its native congener, does not result from the differential cultivation of beneficial or antagonistic rhizosphere microorganisms.

Michigan, Ohio↗