Dominance of Fructose-Associated Fructobacillus in the Gut Microbiome of Bumblebees (Bombus terrestris) Inhabiting Natural Forest Meadows

Bumblebees are key pollinators in agricultural landscapes. However, little is known about how gut microbial communities respond to anthropogenic changes. We used commercially produced colonies of buff-tailed bumblebees (Bombus terrestris) placed in three habitats. Whole guts (midgut, hindgut, and rectum) of B. terrestris specimens were dissected from the body and analyzed using 16S phylogenetic community analysis. We observed significantly different bacterial community composition between the agricultural landscapes (apple orchards and oilseed rape (Brassica napus) fields) and forest meadows, whereas differences in gut communities between the orchards and oilseed rape fields were nonsignificant. Bee-specific bacterial genera such as Lactobacillus, Snodgrassella, and Gilliamella dominated gut communities of B. terrestris specimens. In contrast, the guts of B. terrestris from forest meadows were dominated by fructose-associated Fructobacillus spp. Bacterial communities of workers were the most diverse. At the same time, those of males and young queens were less diverse, possibly reflecting greater exposure to the colony’s inner environment compared to the environment outside the colony, as well as bumblebee age. Our results suggest that habitat quality, exposure to environmental microbes, nectar quality and accessibility, and land use significantly affect gut bacterial composition in B. terrestris.

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Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding Approach

Frontiers in Microbiology ◽

10.3389/fmicb.2018.02301 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 10

Author(s):

Wen Chen ◽

Graham Wilkes ◽

Izhar U. H. Khan ◽

Katarina D. M. Pintar ◽

Janis L. Thomas ◽

...

Keyword(s):

Land Use ◽

Environmental Factors ◽

Bacterial Communities ◽

Agricultural Landscapes

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Endophytic bacterial communities of oilseed rape associate with genotype-specific resistance against Verticillium longisporum

FEMS Microbiology Ecology ◽

10.1093/femsec/fiz188 ◽

2019 ◽

Vol 96 (1) ◽

Cited By ~ 1

Author(s):

Stefanie P Glaeser ◽

Iulian Gabur ◽

Hossein Haghighi ◽

Jens-Ole Bartz ◽

Peter Kämpfer ◽

...

Keyword(s):

Oilseed Rape ◽

Relative Abundance ◽

Bacterial Communities ◽

Quantitative Resistance ◽

Bacterial Community Composition ◽

Phylogenetic Group ◽

Rrna Gene ◽

Host Genotype ◽

Brassica Napus L ◽

Verticillium Longisporum

ABSTRACT Associations of endophytic bacterial community composition of oilseed rape (Brassica napus L.) with quantitative resistance against the soil-borne fungal pathogen Verticillium longisporum was assessed by 16S rRNA gene amplicon sequencing in roots and hypocotyls of four plant lines with contrasting genetic composition in regard to quantitative resistance reactions. The plant compartment was found to be the dominating driving factor for the specificity of bacterial communities in healthy plants. Furthermore, V. longisporum infection triggered a stabilization of phylogenetic group abundance in replicated samples suggesting a host genotype-specific selection. Genotype-specific associations with bacterial phylogenetic group abundance were identified by comparison of plant genotype groups (resistant versus susceptible) and treatment groups (healthy versus V. longisporum-infected) allowing dissection into constitutive and induced directional association patterns. Relative abundance of Flavobacteria, Pseudomonas, Rhizobium and Cellvibrio was associated with resistance/susceptibility. Relative abundance of Flavobacteria and Cellvibrio was increased in resistant genotypes according to their known ecological functions. In contrast, a higher relative abundance of Pseudomonas and Rhizobium, which are known to harbor many species with antagonistic properties to fungal pathogens, was found to be associated with susceptibility, indicating that these groups do not play a major role in genetically controlled resistance of oilseed rape against V. longisporum.

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Participatory Mapping of Demand for Ecosystem Services in Agricultural Landscapes

Agriculture ◽

10.3390/agriculture11121193 ◽

2021 ◽

Vol 11 (12) ◽

pp. 1193

Author(s):

Carmen Schwartz ◽

Mostafa Shaaban ◽

Sonoko Dorothea Bellingrath-Kimura ◽

Annette Piorr

Keyword(s):

Land Use ◽

Ecosystem Services ◽

Agricultural Land ◽

Arable Land ◽

Agricultural Landscapes ◽

The Body ◽

Poor Correlation ◽

Stakeholder Groups ◽

Trade Offs ◽

Stakeholder Workshop

Agricultural land use systems have been optimized for producing provisioning ecosystem services (ES) in the past few decades, often at the expense of regulating and cultural services. Research has focused mainly on the supply side of ES and related trade-offs, but the demand side for regulatory services remains largely neglected. The objective of this paper is to evaluate the usefulness of participatory geographic information system (PGIS) methods for demand assessment in larger rural and agrarian contexts by identifying spatially explicit demand patterns for ES, thereby enlarging the body of participatory approaches to ES-based land use management. Accordingly, we map, assess, and statistically and spatially analyze different demands for five ES by different stakeholder groups in agricultural landscapes in three case studies. The results are presented in a stakeholder workshop and prerequisites for collaborative ES management are discussed. Our results show that poor correlation exists between stakeholder groups and demands for ES; however, arable land constitutes the highest share of the mapped area of demands for the five ES. These results have been validated by both the survey and the stakeholder workshop. Our study concludes that PGIS represents a useful tool to link demand assessments and landscape management systematically, especially for decision support systems.

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Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities

Applied and Environmental Microbiology ◽

10.1128/aem.01443-15 ◽

2015 ◽

Vol 81 (21) ◽

pp. 7448-7459 ◽

Cited By ~ 26

Author(s):

Blaire Steven ◽

Cheryl R. Kuske ◽

La Verne Gallegos-Graves ◽

Sasha C. Reed ◽

Jayne Belnap

Keyword(s):

Climate Change ◽

Land Use ◽

Bacterial Communities ◽

Field Experiments ◽

Metagenomic Sequencing ◽

Small Community ◽

Soil Warming ◽

Bacterial Composition ◽

Soil Bacterial ◽

The Impact

ABSTRACTBiological soil crusts (biocrusts) colonize plant interspaces in many drylands and are critical to soil nutrient cycling. Multiple climate change and land use factors have been shown to detrimentally impact biocrusts on a macroscopic (i.e., visual) scale. However, the impact of these perturbations on the bacterial components of the biocrusts remains poorly understood. We employed multiple long-term field experiments to assess the impacts of chronic physical (foot trampling) and climatic changes (2°C soil warming, altered summer precipitation [wetting], and combined warming and wetting) on biocrust bacterial biomass, composition, and metabolic profile. The biocrust bacterial communities adopted distinct states based on the mechanism of disturbance. Chronic trampling decreased biomass and caused small community compositional changes. Soil warming had little effect on biocrust biomass or composition, while wetting resulted in an increase in the cyanobacterial biomass and altered bacterial composition. Warming combined with wetting dramatically altered bacterial composition and decreasedCyanobacteriaabundance. Shotgun metagenomic sequencing identified four functional gene categories that differed in relative abundance among the manipulations, suggesting that climate and land use changes affected soil bacterial functional potential. This study illustrates that different types of biocrust disturbance damage biocrusts in macroscopically similar ways, but they differentially impact the resident soil bacterial communities, and the communities' functional profiles can differ depending on the disturbance type. Therefore, the nature of the perturbation and the microbial response are important considerations for management and restoration of drylands.

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Soil Type Is the Primary Determinant of the Composition of the Total and Active Bacterial Communities in Arable Soils

Applied and Environmental Microbiology ◽

10.1128/aem.69.3.1800-1809.2003 ◽

2003 ◽

Vol 69 (3) ◽

pp. 1800-1809 ◽

Cited By ~ 480

Author(s):

Martina S. Girvan ◽

Juliet Bullimore ◽

Jules N. Pretty ◽

A. Mark Osborn ◽

Andrew S. Ball

Keyword(s):

Land Use ◽

Organic Matter ◽

Soil Type ◽

Bacterial Communities ◽

Management Practices ◽

Bacterial Community Composition ◽

Arable Soils ◽

Soil Biodiversity ◽

Soil Bacterial Communities ◽

Soil Bacterial

ABSTRACT Degradation of agricultural land and the resulting loss of soil biodiversity and productivity are of great concern. Land-use management practices can be used to ameliorate such degradation. The soil bacterial communities at three separate arable farms in eastern England, with different farm management practices, were investigated by using a polyphasic approach combining traditional soil analyses, physiological analysis, and nucleic acid profiling. Organic farming did not necessarily result in elevated organic matter levels; instead, a strong association with increased nitrate availability was apparent. Ordination of the physiological (BIOLOG) data separated the soil bacterial communities into two clusters, determined by soil type. Denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism analyses of 16S ribosomal DNA identified three bacterial communities largely on the basis of soil type but with discrimination for pea cropping. Five fields from geographically distinct soils, with different cropping regimens, produced highly similar profiles. The active communities (16S rRNA) were further discriminated by farm location and, to some degree, by land-use practices. The results of this investigation indicated that soil type was the key factor determining bacterial community composition in these arable soils. Leguminous crops on particular soil types had a positive effect upon organic matter levels and resulted in small changes in the active bacterial population. The active population was therefore more indicative of short-term management changes.

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From pine to pasture: land use history has long-term impacts on soil bacterial community composition and functional potential

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa041 ◽

2020 ◽

Vol 96 (4) ◽

Author(s):

Syrie M Hermans ◽

Matthew Taylor ◽

Gwen Grelet ◽

Fiona Curran-Cournane ◽

Hannah L Buckley ◽

...

Keyword(s):

Land Use ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Reference Sites ◽

Functional Potential ◽

Soil Bacterial Communities ◽

Soil Bacterial

ABSTRACT Bacterial communities are crucial to soil ecosystems and are known to be sensitive to environmental changes. However, our understanding of how present-day soil bacterial communities remain impacted by historic land uses is limited; implications for their functional potential are especially understudied. Through 16S rRNA gene amplicon and shotgun metagenomic sequencing, we characterized the structure and functional potential of soil bacterial communities after land use conversion. Sites converted from pine plantations to dairy pasture were sampled five- and eight-years post conversion. The bacterial community composition and functional potential at these sites were compared to long-term dairy pastures and pine forest reference sites. Bacterial community composition and functional potential at the converted sites differed significantly from those at reference sites (P = 0.001). On average, they were more similar to those in the long-term dairy sites and showed gradual convergence (P = 0.001). Differences in composition and functional potential were most strongly related to nutrients such as nitrogen, Olsen P and the carbon to nitrogen ratio. Genes related to the cycling of nitrogen, especially denitrification, were underrepresented in converted sites compared to long-term pasture soils. Together, our study highlights the long-lasting impacts land use conversion can have on microbial communities, and the implications for future soil health and functioning.

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Land use in urban areas impacts the composition of soil bacterial communities involved in nitrogen cycling. A case study from Lefkosia (Nicosia) Cyprus

Scientific Reports ◽

10.1038/s41598-021-87623-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Coralea Stephanou ◽

Michalis Omirou ◽

Laurent Philippot ◽

Andreas M. Zissimos ◽

Irene C. Christoforou ◽

...

Keyword(s):

Land Use ◽

Bacterial Community ◽

Bacterial Diversity ◽

Urban Areas ◽

Chemical Elements ◽

Bacterial Community Composition ◽

Sampling Location ◽

Land Use Management ◽

Bacterial Composition ◽

Bacterial Assemblages

AbstractThe different types of land-use and soil lithology in urban and peri-urban areas of modern cities compose a complex mosaic of soil ecosystems. It is largely unknown how these differences result in changes in bacterial community composition and structure as well as in functional guilds involved in N cycling. To investigate the bacterial composition and the proportion of denitrifiers in agricultural, forested, schoolyard and industrial areas, 24 samples were collected from urban and peri-urban sites of Lefkosia. Bacterial diversity and the proportion of denitrifiers were assessed by NGS and qPCR, respectively. Proteobacteria, Actinobacteria, Bacteriodetes, Chloroflexi, Acidobacteria and Planctomycetes were identified as the most dominant phyla across all sites, while agricultural sites exhibited the highest bacterial diversity. Heavy metals such as Co, Pb, V and Al were identified as key factors shaping bacterial composition in industrial and schoolyard sites, while the bacterial assemblages in agricultural and forested sites were associated with Ca. Variance partitioning analysis showed that 10.2% of the bacterial community variation was explained by land use management, 5.1% by chemical elements due to soil lithology, and 1.4% by sampling location. The proportion of denitrifiers varied with land use management. In industrial and schoolyard sites, the abundance of the nosZII bacterial community increased while nirK abundance declined. Our data showed that land use and lithology have a moderate impact on the bacterial assemblages in urban and peri-urban areas of Lefkosia. As the nosZII bacterial community is important to the N2O sink capacity of soils, it would be interesting to elucidate the factors contributing to the proliferation of the nosZII clade in these soils.

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The Effects of Pavement Types on Soil Bacterial Communities across Different Depths

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph16101805 ◽

2019 ◽

Vol 16 (10) ◽

pp. 1805 ◽

Cited By ~ 1

Author(s):

Weiwei Yu ◽

Yinhong Hu ◽

Bowen Cui ◽

Yuanyuan Chen ◽

Xiaoke Wang

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Shannon Index ◽

Soil Bacterial Community ◽

Total Carbon ◽

Bacterial Composition ◽

Soil Bacterial ◽

Micro Organisms

Pavements have remarkable effects on topsoil micro-organisms, but it remains unclear how subsoil microbial communities respond to pavements. In this study, ash trees (Fraxinus Chinensis) were planted on pervious pavement (PP), impervious pavement (IPP), and non-pavement (NP) plots. After five years, we determined the soil bacterial community composition and diversity by high-throughput sequencing of the bacterial 16S rRNA gene. The results of our field experiment reveal that the presence of pavement changed soil bacterial community composition and decreased the Shannon index, but had no impact on the Chao 1 at the 0–20 cm layer. However, we achieved the opposite result at a depth of 20–80 cm. Furthermore, there was a significant difference in bacterial community composition using the Shannon index and the Chao 1 at the 80–100 cm layer. Soil total carbon (TC), total nitrogen (TN), available phosphorus (AP), NO3−-N, and available potassium (AK) were the main factors that influenced soil bacterial composition and diversity across different pavements. Soil bacterial composition and diversity had no notable difference between PP and IPPs at different soil layers. Our results strongly indicate that pavements have a greater impact on topsoil bacterial communities than do subsoils, and PPs did not provide a better habitat for micro-organisms when compared to IPPs in the short term.

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Rhizosphere bacterial communities associated with long-lived perennial prairie plants vary in diversity, composition, and structure

Canadian Journal of Microbiology ◽

10.1139/cjm-2012-0661 ◽

2013 ◽

Vol 59 (7) ◽

pp. 494-502 ◽

Cited By ~ 19

Author(s):

N. Rosenzweig ◽

J.M. Bradeen ◽

Z.J. Tu ◽

S.J. McKay ◽

L.L. Kinkel

Keyword(s):

Community Composition ◽

Plant Species ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Community Analysis ◽

Ecosystem Functions ◽

Individual Plant ◽

Broad Array ◽

Culture Independent

The goal of this research was to investigate the variation in rhizosphere microbial community composition, diversity, and structure among individual Andropogon gerardii Vitman (big bluestem) and Lespedeza capitata Michx. (bush clover). Bacterial communities from the rhizosphere of 10 plants of each species (n = 20 plants total) were explored using a culture-independent pipeline. Microbial communities associated with both host plants had high bacterial diversity within individual plant rhizosphere and taxa unique to individual rhizospheres. Bacterial communities associated with the rhizosphere of A. gerardii were consistently more diverse than those associated with L. capitata, and there were significant differences between plant species in rhizosphere bacterial community composition. Differences included microbial taxa with no known functional relationship with their preferred host species, including sulfide-methylating obligate anaerobes (Holophaga), complete denitrifiers (Rhodoplanes), sludge inhabitants (Ktedonobacter), and nitrate oxidizers (Nitrospira). These results suggest the potential for plant species to have significant impacts on a broad array of ecosystem functions (e.g., cycling of carbon, nitrogen sulfurs, metals, and trace elements) via their selective impacts on soil microbes. However, sequence-based community analysis and the corresponding lack of intact microbial cultures limits understanding of the potential influences of enriched microbial taxa on plant hosts and their roles in ecosystem functioning.

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Consistent bacterial responses to land use change across the tropics

10.1101/600924 ◽

2019 ◽

Cited By ~ 2

Author(s):

Ian AB Petersen ◽

Kyle M Meyer ◽

Brendan JM Bohannan

Keyword(s):

Land Use ◽

Land Use Change ◽

Bacterial Communities ◽

Tropical Rainforest ◽

Meta Analysis ◽

Bacterial Community Composition ◽

Agricultural Practices ◽

Alpha Diversity ◽

Tropical Rainforests ◽

The Tropics

AbstractBacterial communities are a major component of global diversity and are intimately involved in most terrestrial biogeochemical processes. Despite their importance, we know far less about the response of bacteria to human-induced environmental change than we do about other organisms. Understanding the response of organisms to land use change is especially pressing for tropical rainforests, which are being altered at a higher rate than any other ecosystem. Here, we conduct a meta-analysis of studies performed in each of the major tropical rainforest regions to ask whether there are consistent responses of belowground bacterial communities to the conversion of tropical rainforest to agriculture. Remarkably, we find common responses despite wide variation across studies in the types of agriculture practiced and the research methodology used to study land use change. These responses include changes in the relative abundance of phyla, most notably decreases in Acidobacteria and Proteobacteria and increases in Actinobacteria, Chloroflexi and Firmicutes. We also find that alpha diversity (at the scale of single soil cores), consistently increases with ecosystem conversion. These consistent responses suggest that, while there is great diversity in agricultural practices across the tropics, common features such as the use of slash-and-burn tactics have the potential to alter bacterial community composition and diversity belowground.

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