| 1. |
- Bates, Scott T., et al.
(författare)
-
Meeting Report: Fungal ITS Workshop (October 2012)
- 2013
-
Ingår i: Standards in Genomic Sciences. - : Springer Science and Business Media LLC. - 1944-3277. ; 8:1, s. 118-123
-
Tidskriftsartikel (refereegranskat)abstract
- This report summarizes a meeting held in Boulder, CO USA (19–20 October 2012) on fungal community analyses using ultra-high-throughput sequencing of the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA (rRNA) genes. The meeting was organized as a two-day workshop, with the primary goal of supporting collaboration among researchers for improving fungal ITS sequence resources and developing recommendations for standard ITS primers for the research community.
|
|
| 2. |
- Fountain‐Jones, Nicholas M., et al.
(författare)
-
Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions
- 2024
-
Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 33:2
-
Tidskriftsartikel (refereegranskat)abstract
- The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores common challenges, methodological advancements, and future directions in the field. Key research areas include understanding the drivers of microbiome community assembly, linking microbiome composition to host genetics, exploring microbial functions, transience and spatial partitioning, and disentangling non-bacterial components of the microbiome. Methodological advancements, such as quantifying absolute abundances, sequencing complete genomes, and utilizing novel statistical approaches, are also useful tools for understanding complex microbial diversity patterns. Our aims are to encourage robust practices in microbiome studies and inspire researchers to explore the next frontier of this rapidly changing field.
|
|
| 3. |
- Ingels, Jeroen, et al.
(författare)
-
Chapter 7M Abyssal Plains
- 2021
-
Ingår i: The Second World Ocean Assessment : WOA II. - New York : United Nations. ; , s. 453-476
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- • The abyss lies between 3 and 6 km water depth and covers more of the Earth’s sur- face than all other habitats combined. • The present chapter is the first in the World Ocean Assessment that is dedicated to the abyss, covering biodiversity, regional dif- ferences, biogeography, and changes and impacts as a result of natural stressors and anthropogenic activity. • Abyssal biodiversity is not well under- stood, and many gaps exist in the current understanding of abyssal evolution and biogeography, as well as the distributions, connectivity and responses of organisms to changing conditions. • Fragmentary knowledge of abyssal taxono- my is largely the result of difficulties in sam- pling the vast and remote area and, hence, limited research effort, which hinders the advancement of scientific knowledge. • Most abyssal environments support the processes that drive deep-sea and global ecosystem functioning and are linked closely to surface production and pelagic processes. • Climate change and anthropogenic impacts affect the abyss, despite its remoteness.
|
|
| 4. |
- Leray, Matthieu, et al.
(författare)
-
Natural experiments and long-term monitoring are critical to understand and predict marine host–microbe ecology and evolution
- 2021
-
Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 19:8, s. e3001322-e3001322
-
Tidskriftsartikel (refereegranskat)abstract
- Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host’s physiological capacities; however, the identity and functional role(s) of key members of the microbiome (“core microbiome”) in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems’ capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts’ plastic and adaptive responses to environmental change requires (i) recognizing that individual host–microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions.
|
|
| 5. |
- Nascimento, Francisco J. A., et al.
(författare)
-
Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structure
- 2019
-
Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 2
-
Tidskriftsartikel (refereegranskat)abstract
- Ecological interactions between aquatic plants and sediment communities can shape the structure and function of natural systems. Currently, we do not fully understand how sea- grass habitat degradation impacts the biodiversity of belowground sediment communities. Here, we evaluated indirect effects of disturbance of seagrass meadows on meiobenthic community composition, with a five-month in situ experiment in a tropical seagrass meadow. Disturbance was created by reducing light availability (two levels of shading), and by mimicking grazing events (two levels) to assess impacts on meiobenthic diversity using high- throughput sequencing of 18S rRNA amplicons. Both shading and simulated grazing had an effect on meiobenthic community structure, mediated by seagrass-associated biotic drivers and sediment abiotic variables. Additionally, shading substantially altered the trophic structure of the nematode community. Our findings show that degradation of seagrass meadows can alter benthic community structure in coastal areas with potential impacts to ecosystem functions mediated by meiobenthos in marine sediments.
|
|
| 6. |
- Nascimento, Francisco J. A., et al.
(författare)
-
Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing
- 2018
-
Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8
-
Tidskriftsartikel (refereegranskat)abstract
- Understanding how biodiversity changes in time and space is vital to assess the effects of environmental change on benthic ecosystems. Due to the limitations of morphological methods, there has been a rapid expansion in the application of high-throughput sequencing methods to study benthic eukaryotic communities. However, the effect of sample size and small-scale spatial variation on the assessment of benthic eukaryotic diversity is still not well understood. Here, we investigate the effect of different sample volumes in the genetic assessment of benthic metazoan and non-metazoan eukaryotic community composition. Accordingly, DNA was extracted from five different cumulative sediment volumes comprising 100% of the top 2 cm of five benthic sampling cores, and used as template for Ilumina MiSeq sequencing of 18 S rRNA amplicons. Sample volumes strongly impacted diversity metrics for both metazoans and non-metazoan eukaryotes. Beta-diversity of treatments using smaller sample volumes was significantly different from the beta-diversity of the 100% sampled area. Overall our findings indicate that sample volumes of 0.2 g (1% of the sampled area) are insufficient to account for spatial heterogeneity at small spatial scales, and that relatively large percentages of sediment core samples are needed for obtaining robust diversity measurement of both metazoan and non-metazoan eukaryotes.
|
|
