scholarly journals Invasive Grass Dominance over Native Forbs Is Linked to Shifts in the Bacterial Rhizosphere Microbiome

2021 ◽  
Author(s):  
Marina L. LaForgia ◽  
Hannah Kang ◽  
Cassandra L. Ettinger
Keyword(s):  
Bacterial Community ◽  
Plant Biomass ◽  
Plant Competition ◽  
Its Region ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Community Structures ◽  
Invasive Grass ◽  
Soil Nutrition ◽  
Annual Grasses

AbstractRhizosphere microbiomes have received growing attention in recent years for their role in plant health, stress tolerance, soil nutrition, and invasion. Still, relatively little is known about how these microbial communities are altered under plant competition, and even less about whether these shifts are tied to competitive outcomes between native and invasive plants. We investigated the structure and diversity of rhizosphere bacterial and fungal microbiomes of native annual forbs and invasive annual grasses grown in a shade-house both individually and in competition using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. We assessed how differentially abundant microbial families correlate to plant biomass under competition. We find that bacterial diversity and structure differ between native forbs and invasive grasses, but fungal diversity and structure do not. Furthermore, bacterial community structures under competition are distinct from individual bacterial community structures. We also identified five bacterial families that varied in normalized abundance between treatments and that were correlated with plant biomass under competition. We speculate that invasive grass dominance over these natives may be partially due to effects on the rhizosphere community, with changes in specific bacterial families potentially benefiting invaders at the expense of natives.

scholarly journals Competitive outcomes between native and invasive plants are linked to shifts in the bacterial rhizosphere microbiome

2021 ◽  
Author(s):  
Marina L LaForgia ◽  
Hannah Kang ◽  
Cassandra L Ettinger
Keyword(s):  
Bacterial Community ◽  
Invasive Plant ◽  
Plant Competition ◽  
Its Region ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Community Structures ◽  
Competitive Response ◽  
Species Dominance ◽  
Competitive Outcomes

Background: Rhizosphere microbiomes have received growing attention in recent years for their role in plant health, stress tolerance, soil nutrition, and invasive species dominance. Still, relatively little is known about how these microbial communities are altered under plant competition, and even less about whether these shifts are tied to competitive outcomes between native and invasive plant species. We investigated the structure and diversity of rhizosphere bacterial and fungal microbiomes of native annual forbs and invasive annual grasses individually and in competition using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. We assessed how significant shifts in key microbial families correlate to plant competitive responses through changes in biomass (log competitive response ratios). Results: We find that bacterial diversity and structure differ between invasive grasses and native forbs, but fungal diversity and structure do not. Further, bacterial community structures under competition are distinct from both individual forb and grass bacterial community structures. We identified four bacterial families (Burkholderiaceae, Methylophilaceae, Clostridiaceae_1, and Fibrobacteraceae) that varied in relative abundance between treatments and that were significantly correlated with plant competitive responses. Conclusions: Invasive grass dominance may be partially due to effects on the rhizosphere community of native forbs, with changes in specific bacterial families potentially benefiting grasses at the expense of native forbs. Our study underscores the importance of considering plant-rhizosphere interactions for understanding outcomes of plant invasion on grassland ecosystems.

scholarly journals Relative and quantitative rhizosphere microbiome profiling result in distinct abundance patterns

2021 ◽  
Author(s):  
Hamed Azarbad ◽  
Julien Tremblay ◽  
Luke D. Bainard ◽  
Etienne Yergeau
Keyword(s):  
Water Stress ◽  
Relative Abundance ◽  
Its Region ◽  
Cost Effective ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Real Time Quantitative Pcr ◽  
Rhizosphere Microbiome ◽  
History Of ◽  
Almost All

AbstractNext-generation sequencing is recognized as one of the most popular and cost-effective way of characterizing microbiome in multiple samples. However, most of the currently available amplicon sequencing approaches are inherently limited, as they are often presented based on the relative abundance of microbial taxa, which may not fully represent actual microbiome profiles. Here, we combined amplicon sequencing (16S rRNA gene for bacteria and ITS region for fungi) with real-time quantitative PCR (qPCR) to characterize the rhizosphere microbiome of wheat. We show that the increase in relative abundance of major microbial phyla does not necessarily result in an increase in abundance. One striking observation when comparing relative and quantitative abundances was a substantial increase in the abundance of almost all phyla associated with the rhizosphere of plants grown in soil with no history of water stress as compared with the rhizosphere of plants growing in soil with a history of water stress, which was in contradiction with the trends observed in the relative abundance data. Our results suggest that the estimated absolute abundance approach gives a different perspective than the relative abundance approach, providing complementary information that helps to better understand the rhizosphere microbiome.

scholarly journals Continental-Scale Microbiome Study Reveals Different Environmental Characteristics Determining Microbial Richness, Composition, and Quantity in Hotel Rooms

mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Xi Fu ◽  
Yanling Li ◽  
Qianqian Yuan ◽  
Gui-hong Cai ◽  
Yiqun Deng ◽  
...  
Keyword(s):  
Heavy Traffic ◽  
Its Region ◽  
Amplicon Sequencing ◽  
Compositional Variation ◽  
Rrna Gene ◽  
Environmental Characteristics ◽  
Negatively Associated ◽  
Continental Scale ◽  
Absolute Quantity

ABSTRACT Culture-independent microbiome surveys have been conducted in homes, hospitals, schools, kindergartens and vehicles for public transport, revealing diverse microbial distributions in built environments. However, microbiome composition and the associated environmental characteristics have not been characterized in hotel environments. We presented here the first continental-scale microbiome study of hotel rooms (n = 68) spanning Asia and Europe. Bacterial and fungal communities were described by amplicon sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region and quantitative PCR. Similar numbers of bacterial (4,344) and fungal (4,555) operational taxonomic units were identified in the same sequencing depth, but most fungal taxa showed a restricted distribution compared to bacterial taxa. Aerobic, ubiquitous bacteria dominated the hotel microbiome with compositional similarity to previous samples from building and human nasopharynx environments. The abundance of Aspergillus was negatively correlated with latitude and accounted for ∼80% of the total fungal load in seven low-latitude hotels. We calculated the association between hotel microbiome and 16 indoor and outdoor environmental characteristics. Fungal composition and absolute quantity showed concordant associations with the same environmental characteristics, including latitude, quality of the interior, proximity to the sea, and visible mold, while fungal richness was negatively associated with heavy traffic (95% confidence interval [CI] = −127.05 to −0.25) and wall-to-wall carpet (95% CI = −47.60 to −3.82). Bacterial compositional variation was associated with latitude, quality of the interior, and floor type, while bacterial richness was negatively associated with recent redecoration (95% CI −179.00 to −44.55) and mechanical ventilation (95% CI = −136.71 to −5.12). IMPORTANCE This is the first microbiome study to characterize the microbiome data and associated environmental characteristics in hotel environments. In this study, we found concordant variation between fungal compositional variation and absolute quantity and discordant variation between community variation/quantity and richness. Our study can be used to promote hotel hygiene standards and provide resource information for future microbiome and exposure studies associated with health effects in hotel rooms.

Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish

2019 ◽  
Author(s):  
Lara Parata ◽  
Shaun Nielsen ◽  
Xing Xing ◽  
Torsten Thomas ◽  
Suhelen Egan ◽  
...  
Keyword(s):  
Coral Reef ◽  
Gastrointestinal Tract ◽  
Bacterial Community ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Food Source ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Symbionts ◽  
Adult Fish

Abstract Herbivorous fishes play important ecological roles in coral reefs by consuming algae that can otherwise outcompete corals, but we know little about the gut microbiota that facilitates this process. This study focussed on the gut microbiota of an ecologically important coral reef fish, the convict surgeonfish Acanthurus triostegus. We sought to understand how the microbiome of this species varies along its gastrointestinal tract and how it varies between juvenile and adult fish. Further, we examined if the bacteria associated with the diet consumed by juveniles contributes to the gut microbiota. 16S rRNA gene amplicon sequencing showed that bacterial communities associated with the midgut and hindgut regions were distinct between adults and juveniles, however, no significant differences were seen for gut wall samples. The microbiota associated with the epilithic algal food source was similar to that of the juvenile midgut and gut wall but differed from the microbiome of the hindgut. A core bacterial community including members of taxa Epulopiscium and Brevinemataceae was observed across all gastrointestinal and diet samples, suggesting that these bacterial symbionts can be acquired by juvenile convict surgeonfish horizontally via their diet and then are retained into adulthood.

scholarly journals A converging subset of soil bacterial taxa is permissive to the IncP-1 plasmid pKJK5 across a range of soil copper contamination

2020 ◽  
Vol 96 (11) ◽  
Author(s):  
Jianxiao Song ◽  
Uli Klümper ◽  
Leise Riber ◽  
Arnaud Dechesne ◽  
Barth F Smets ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Amplicon Sequencing ◽  
Plasmid Transfer ◽  
Rrna Gene ◽  
Long Term Effects ◽  
Cu Contamination ◽  
Soil Bacterial

ABSTRACT Stressors like metals or antibiotics can affect bacterial community permissiveness for plasmid uptake, but there is little knowledge about long-term effects of such stressors on the evolution of community permissiveness. We assessed the effect of more than 90 years of soil Cu contamination on bacterial community permissiveness (i.e. uptake ability) toward a gfp-tagged IncP-1 plasmid (pKJK5) introduced via an Escherichia coli donor. Plasmid transfer events from the donor to the recipient soil bacterial community were quantified and transconjugants were subsequently isolated by fluorescence activated cell sorting and identified by 16S rRNA gene amplicon sequencing. Transfer frequency of plasmid pKJK5 was reduced in bacterial communities extracted from highly Cu contaminated (4526 mg kg−1) soil compared to corresponding communities extracted from moderately (458 mg kg−1) Cu contaminated soil and a low Cu reference soil (15 mg kg−1). The taxonomic composition of the transconjugal pools showed remarkable similarities irrespective of the degree of soil Cu contamination and despite contrasting compositions of the extracted recipient communities and the original soil communities. Permissiveness assessed at the level of individual operational taxonomic units (OTUs; 16S rRNA gene 97% sequence similarity threshold) was only slightly affected by soil Cu level and high replicate variability of OTU-level permissiveness indicated a role of stochastic events in IncP-1 plasmid transfer or strain-to-strain permissiveness variability.

scholarly journals A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Siwen Deng ◽  
Heidi M.-L. Wipf ◽  
Grady Pierroz ◽  
Ted K. Raab ◽  
Rajnish Khanna ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Amendment ◽  
Bacterial Community Composition ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Microbiome ◽  
Plant Growth Promoting ◽  
Miseq Platform ◽  
Soil Rhizosphere

AbstractDespite growing interest in utilizing microbial-based methods for improving crop growth, much work still remains in elucidating how beneficial plant-microbe associations are established, and what role soil amendments play in shaping these interactions. Here, we describe a set of experiments that test the effect of a commercially available soil amendment, VESTA, on the soil and strawberry (Fragaria x ananassa Monterey) root bacterial microbiome. The bacterial communities of the soil, rhizosphere, and root from amendment-treated and untreated fields were profiled at four time points across the strawberry growing season using 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform. In all sample types, bacterial community composition and relative abundance were significantly altered with amendment application. Importantly, time point effects on composition are more pronounced in the root and rhizosphere, suggesting an interaction between plant development and treatment effect. Surprisingly, there was slight overlap between the taxa within the amendment and those enriched in plant and soil following treatment, suggesting that VESTA may act to rewire existing networks of organisms through an, as of yet, uncharacterized mechanism. These findings demonstrate that a commercial microbial soil amendment can impact the bacterial community structure of both roots and the surrounding environment.

scholarly journals 16S rRNA gene analyses of bacterial community structures in the soils of evergreen broad-leaved forests in south-west China

2006 ◽  
Vol 58 (2) ◽  
pp. 247-259 ◽  
Author(s):  
On Chim Chan ◽  
Xiaodong Yang ◽  
Yun Fu ◽  
Zhili Feng ◽  
Liqing Sha ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Community Structures ◽  
West China ◽  
South West

scholarly journals Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing

PLoS ONE ◽  
2012 ◽  
Vol 7 (8) ◽  
pp. e41606 ◽  
Author(s):  
Sebastian Jünemann ◽  
Karola Prior ◽  
Rafael Szczepanowski ◽  
Inga Harks ◽  
Benjamin Ehmke ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Ion Torrent ◽  
Community Shift

scholarly journals Impact of Harvest on Switchgrass Leaf Microbial Communities

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 22
Author(s):  
Esther Singer ◽  
Elizabeth M. Carpenter ◽  
Jason Bonnette ◽  
Tanja Woyke ◽  
Thomas E. Juenger
Keyword(s):  
Microbial Community ◽  
Panicum Virgatum ◽  
Leaf Surface ◽  
Its Region ◽  
Amplicon Sequencing ◽  
Biofuel Production ◽  
Rrna Gene ◽  
Community Studies ◽  
Community Members ◽  
Increase Productivity

Switchgrass is a promising feedstock for biofuel production, with potential for leveraging its native microbial community to increase productivity and resilience to environmental stress. Here, we characterized the bacterial, archaeal and fungal diversity of the leaf microbial community associated with four switchgrass (Panicum virgatum) genotypes, subjected to two harvest treatments (annual harvest and unharvested control), and two fertilization levels (fertilized and unfertilized control), based on 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. Leaf surface and leaf endosphere bacterial communities were significantly different with Alphaproteobacteria enriched in the leaf surface and Gammaproteobacteria and Bacilli enriched in the leaf endosphere. Harvest treatment significantly shifted presence/absence and abundances of bacterial and fungal leaf surface community members: Gammaproteobacteria were significantly enriched in harvested and Alphaproteobacteria were significantly enriched in unharvested leaf surface communities. These shifts were most prominent in the upland genotype DAC where the leaf surface showed the highest enrichment of Gammaproteobacteria, including taxa with 100% identity to those previously shown to have phytopathogenic function. Fertilization did not have any significant impact on bacterial or fungal communities. We also identified bacterial and fungal taxa present in both the leaf surface and leaf endosphere across all genotypes and treatments. These core taxa were dominated by Methylobacterium, Enterobacteriaceae, and Curtobacterium, in addition to Aureobasidium, Cladosporium, Alternaria and Dothideales. Local core leaf bacterial and fungal taxa represent promising targets for plant microbe engineering and manipulation across various genotypes and harvest treatments. Our study showcases, for the first time, the significant impact that harvest treatment can have on bacterial and fungal taxa inhabiting switchgrass leaves and the need to include this factor in future plant microbial community studies.

scholarly journals Bacterial community shift in nutrient-treated oil-bearing sandstones from the subsurface strata of an onshore oil reservoir and its potential use in Microbial Enhanced Oil Recovery

2018 ◽  
Author(s):  
Thanachai Phetcharat ◽  
Pinan Dawkrajai ◽  
Thararat Chitov ◽  
Pisanu Wongpornchai ◽  
Schradh Saenton ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Enhanced Oil Recovery ◽  
Oil Recovery ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Microbial Enhanced Oil Recovery ◽  
Nutrient Treatment ◽  
Chemical Structures

AbstractMicrobial Enhanced Oil Recovery (MEOR) is a promising strategy to improve recovery of residual oil in reservoirs, which can be performed by promoting specific indigenous microorganisms. In this study, bacterial communities and the effects of elemental nutrient treatment of oil-bearing sandstone cores originated from six oil wells of an onshore reservoir was determined by tagged 16S rRNA gene amplicon sequencing, using Ion Torrent Metagenomic Sequencing Analysis. A total number of sequences were taxonomically classified into 43 phyla, 320 families, and 584 genera, with the dominant bacterial populations being related to Deinococcus-Thermus, and Betaproteobacteria. The nutrient treatment resulted in markedly increase in the relative abundance of Gammaproteobacteria. Thermus, Acinetobacter, and Pseudomonas were the most abundant genera. To our knowledge, this is the first report on the effect of elemental nutrients on alteration of bacteria communities attached to the oil-bearing rock. It provides comprehensive data on bacterial, physical, and chemical structures within a reservoir and demonstrates how these parameters can be co-analyzed to serve as a basis for designing a MEOR process. It also provides a model of how a bacterial community in reservoirs’ strata can be altered by nutrient treatment to enhance the efficiency of MEOR applications.

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