Environmental Microbiome
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Exploring virus-host-environment interactions in a chemotrophic-based underground estuary
Environmental Microbiome - Tập 19 - Trang 1-13 - 2024
Viruses play important roles in modulating microbial communities and influencing
global biogeochemistry. There is now growing interest in characterising their
ecological roles across diverse biomes. However, little is known about viral
ecology in low-nutrient, chemotrophic-based environments. In such ecosystems,
virus-driven manipulation of nutrient cycles might have profound impacts across
trophi...
Performance evaluation of a new custom, multi-component DNA isolation method optimized for use in shotgun metagenomic sequencing-based aerosol microbiome research
Environmental Microbiome - Tập 15 - Trang 1-23 - 2020
Aerosol microbiome research advances our understanding of bioaerosols, including
how airborne microorganisms affect our health and surrounding environment.
Traditional microbiological/molecular methods are commonly used to study
bioaerosols, but do not allow for generic, unbiased microbiome profiling. Recent
studies have adopted shotgun metagenomic sequencing (SMS) to address this issue.
However, ...
Metapangenomics of wild and cultivated banana microbiome reveals a plethora of host-associated protective functions
Environmental Microbiome - Tập 18 Số 1
Abstract Background Microbiomes are critical to plants, promoting growth,
elevating stress tolerance, and expanding the plant’s metabolic repertoire with
novel defense pathways. However, generally microbiomes within plant tissues,
which intimately interact with their hosts, remain poorly characterized. These
endospheres have become a focus in banana (Musa spp.)—an important plant for
study of micr...
Metagenomic assembly reveals hosts and mobility of common antibiotic resistome in animal manure and commercial compost
Environmental Microbiome - Tập 17 - Trang 1-15 - 2022
Antibiotics and antibiotic resistance genes (ARGs) used in intensive animal
farming threaten human health worldwide; however, the common resistome, ARG
mobility, and ARG host composition in different animal manures and mixed manure
composts remain unclear. In the present study, metagenomic assembly and
cross-sample mapping were used to comprehensively decipher the common resistome
and its potentia...
Wallace’s line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria
Environmental Microbiome - Tập 19 Số 1
Abstract Background The processes that shape microbial biogeography are not well
understood, and concepts that apply to macroorganisms, like dispersal barriers,
may not affect microorganisms in the same predictable ways. To better understand
how known macro-scale biogeographic processes can be applied at micro-scales, we
examined seagrass associated microbiota on either side of Wallace’s line to
d...
Coupled DNA-labeling and sequencing approach enables the detection of viable-but-non-culturable Vibrio spp. in irrigation water sources in the Chesapeake Bay watershed
Environmental Microbiome - Tập 16 - Trang 1-13 - 2021
Nontraditional irrigation water sources (e.g., recycled water, brackish water)
may harbor human pathogens, including Vibrio spp., that could be present in a
viable-but-nonculturable (VBNC) state, stymieing current culture-based detection
methods. To overcome this challenge, we coupled 5-bromo-2′-deoxyuridine (BrdU)
labeling, enrichment techniques, and 16S rRNA sequencing to identify
metabolically-...
Co-occurrence of planktonic bacteria and archaea affects their biogeographic patterns in China’s coastal wetlands
Environmental Microbiome - Tập 16 - Trang 1-12 - 2021
Planktonic bacteria and archaea play a key role in maintaining ecological
functions in aquatic ecosystems; however, their biogeographic patterns and
underlying mechanisms have not been well known in coastal wetlands including
multiple types and at a large space scale. Therefore, planktonic bacteria and
archaea and related environmental factors were investigated in twenty-one
wetlands along China’s...
The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant–microbe interactions
Environmental Microbiome - Tập 18 - Trang 1-26 - 2023
As holobiont, a plant is intrinsically connected to its microbiomes. However,
some characteristics of these microbiomes, such as their taxonomic composition,
biological and evolutionary role, and especially the drivers that shape them,
are not entirely elucidated. Reports on the microbiota of Arabidopsis thaliana
first appeared more than ten years ago. However, there is still a lack of a
comprehen...
Alternative approaches to identify core bacteria in Fucus distichus microbiome and assess their distribution and host-specificity
Environmental Microbiome - Tập 17 Số 1 - Trang 1-15 - 2022
Identifying meaningful ecological associations between host and components of
the microbiome is challenging. This is especially true for hosts such as marine
macroalgae where the taxonomic composition of the microbiome is highly diverse
and variable in space and time. Identifying core taxa is one way forward but
there are many methods and thresholds in use. This study leverages a large
dataset of ...
Land use modification causes slow, but predictable, change in soil microbial community composition and functional potential
Environmental Microbiome - Tập 18 - Trang 1-16 - 2023
Bacterial communities are critical to ecosystem functioning and sensitive to
their surrounding physiochemical environment. However, the impact of land use
change on microbial communities remains understudied. We used 16S rRNA gene
amplicon sequencing and shotgun metagenomics to assess soil microbial
communities' taxonomic and functional responses to land use change. We compared
data from long-term...
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