| 1. |
- Alneberg, Johannes, et al.
(author)
-
BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
-
Other publication (other academic/artistic)abstract
- The Baltic Sea is one of the world’s largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within microbial ecosystems, but are computationally heavy to perform. We here present the BAltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.
|
|
| 2. |
- Alneberg, Johannes, et al.
(author)
-
BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
- 2018
-
In: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 5
-
Journal article (peer-reviewed)abstract
- The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset. [GRAPHICS] .
|
|
| 3. |
- Capo, Eric, et al.
(author)
-
Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations
- 2021
-
In: Quaternary. - : MDPI. - 2571-550X. ; 4:1
-
Research review (peer-reviewed)abstract
- The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
|
|
| 4. |
- Hötzinger, Matthias, et al.
(author)
-
Dynamics of Baltic Sea phages driven by environmental changes
- 2022
-
In: Environmental Microbiology. - : John Wiley & Sons. - 1462-2912 .- 1462-2920. ; 23:8, s. 4576-4594
-
Journal article (peer-reviewed)abstract
- Phage predation constitutes a major mortality factor for bacteria in aquatic ecosystems, and thus, directly impacts nutrient cycling and microbial community dynamics. Yet, the population dynamics of specific phages across time scales from days to months remain largely unexplored, which limits our understanding of their influence on microbial succession. To investigate temporal changes in diversity and abundance of phages infecting particular host strains, we isolated 121 phage strains that infected three bacterial hosts during a Baltic Sea mesocosm experiment. Genome analysis revealed a novel Flavobacterium phage genus harboring gene sets putatively coding for synthesis of modified nucleotides and glycosylation of bacterial cell surface components. Another novel phage genus revealed a microdiversity of phage species that was largely maintained during the experiment and across mesocosms amended with different nutrients. In contrast to the newly described Flavobacterium phages, phages isolated from a Rheinheimera strain were highly similar to previously isolated genotypes, pointing to genomic consistency in this population. In the mesocosm experiment, the investigated phages were mainly detected after a phytoplankton bloom peak. This concurred with recurrent detection of the phages in the Baltic Proper during summer months, suggesting an influence on the succession of heterotrophic bacteria associated with phytoplankton blooms.
|
|
| 5. |
- Ismagilova, Alina, et al.
(author)
-
Ecotoxicity of isosorbide acrylate and methacrylate monomers and corresponding polymers
- 2023
-
In: Green Chemistry. - 1463-9270. ; 25:4, s. 1626-1634
-
Journal article (peer-reviewed)abstract
- Isosorbide is a well-investigated and accessible biomass-derived compound that has found wide use in medicine, cosmetics, and material sciences. The efforts to employ this rigid bicyclic diol as a sustainable building block in high-performance biobased plastics for, e.g., the engineering, coating, and packaging sectors have grown sharply in recent years. Due to the biomass origin, there is an implicit assumption of a low toxicity and an environmentally benign nature of isosorbide-derived plastics. In the present work, the ecotoxicity of isosorbide acrylate and methacrylate monomers and the corresponding poly(meth)acrylates, as well as industrially produced latexes from these monomers, were evaluated towards bacteria (Escherichia coli, Aliivibrio fischeri), vascular plants (Spirodela polyrhiza) and invertebrates (Thamnocephalus platyurus) using widely acknowledged test assays. The measured half maximal effective concentration (EC50) values indicate that the chemically reactive isosorbide acrylate monomers are toxic towards higher multicellular organisms (S. polyrhiza and T. platyurus, EC50 ~9 mg L-1) and moderately toxic towards bacteria (E. coli), whereas the corresponding methacrylate monomers can be considered as practically harmless or harmless on the same test assays. Corresponding isosorbide polyacrylate and polymethacrylate polymers are harmless towards the tested organisms (EC50 > 1000 mg L-1), except towards E. coli, where two polymers are classified as practically harmless (EC50 = 374 and 514 mg L-1). Moreover, industrially produced isosorbide methacrylate derived latexes can be classified as harmless based on this study.
|
|
| 6. |
- Karlsson, Christofer M. G., et al.
(author)
-
Metatranscriptomic analysis uncovers divergent responses of Baltic Sea bacteria to forest and agriculture river loadings
-
Other publication (other academic/artistic)abstract
- Climate change is predicted to induce substantial changes in precipitation patterns across the globe. In Northern Europe, precipitation is expected to increase more than the global average (particularly in northern Scandinavia), causing increased river runoff. The Baltic Sea is one of the largest brackish environments on earth with a catchment area that spans 14 countries, encompassing primarily forested areas and agricultural landscapes. Despite the acknowledged role of marine bacteria in nutrient cycling, there is a lack of knowledge in their metabolic responses to inorganic and organic nutrient loading from riverine runoff. We investigated the bacterial growth and gene expression responses in a mesocosm experiment in which river water from boreal forest- (enriched in humic substances) or agriculture- influenced catchment areas were added to Baltic Sea Proper water. The riverine nutrient input triggered extensive phytoplankton blooms and bacterial growth, most notably in the agriculture river treatment. Interestingly, bacterial gene expression analysis (metatranscriptomics) showed similar responses to agriculture and humic river inputs at the start of the experiment (before the phytoplankton bloom), but expression patterns diverged significantly upon bloom senescence.Notably, transcripts associated with phosphate metabolism were significantly enriched , whereas transcripts related to nitrogen metabolism were significantly lower in the agriculture river treatment compared to the boreal forest river treatment. The opposite pattern was observed in the boreal forest river water treatment. Overall, our results showed that interactions between river nutrient loading and phytoplankton organic matter are important in regulating bacterial activities and responses at the molecular level. This suggests that bacterial transformations of organic matter and nutrient cycling in coastal waters and estuarine environments are sensitive to changes in precipitation patterns in a catchment area-dependent manner.
|
|
| 7. |
- Kisand, Veljo, et al.
(author)
-
Bacterial freshwater species successfully immigrate to the brackish water environment in the northern Baltic
- 2005
-
In: Limnology and Oceanography. - : American Society of Limnology and Oceanography. - 0024-3590 .- 1939-5590. ; 50:3, s. 945-956
-
Journal article (peer-reviewed)abstract
- We studied the distribution and seasonal dynamics of five species from the genus Flavobacterium and one species from the genus Marinomonas over the course of a year along a northern Baltic Sea river-marine transect. All of the species had been previously demonstrated as important consumers of riverine dissolved organic carbon. Quantitative DNA-DNA hybridization data showed that two of the Flavobacterium spp. and the Marinomonas sp. had highest abundance in the river water (maximum 20,000 cells ml-1), with maximum relative abundance of 0.5-2.5% of the bacterial community. These species declined in abundance from the river to the estuary and the offshore site. Abundance and dynamics in the estuarine environment suggested successful immigration of freshwater bacteria, accompanied by growth in the brackish water environment. Two of the three abundant species showed high cell numbers also during late autumn to early spring in the estuary, indicating a selective advantage when riverine dissolved organic carbon was the main carbon source. The remaining three species showed more episodic abundance close to the detection limit of the method, providing weaker evidence of occurrence in the freshwater environment. Some bacterioplankton consuming riverine organic carbon in the brackish water environment in the northern Baltic are therefore freshwater species, with a selective advantage during winter.
|
|
| 8. |
- Kisand, Veljo, et al.
(author)
-
Combining culture-dependent and -independent methodologies for estimation of richness of estuarine bacterioplankton consuming riverine dissolved organic matter
- 2003
-
In: Applied and Environmental Microbiology. - : American Society for Microbiology. - 0099-2240 .- 1098-5336. ; 69:6, s. 3607-3616
-
Journal article (peer-reviewed)abstract
- Three different methods for analyzing natural microbial community diversity were combined to maximize an estimate of the richness of bacterioplankton catabolizing riverine dissolved organic matter (RDOM). We also evaluated the ability of culture-dependent quantitative DNA-DNA hybridization, a 16S rRNA gene clone library, and denaturing gradient gel electrophoresis (DGGE) to detect bacterial taxa in the same sample. Forty-two different cultivatable strains were isolated from rich and poor solid media. In addition, 50 unique clones were obtained by cloning of the bacterial 16S rDNA gene amplified by PCR from the community DNA into an Escherichia coli vector. Twenty-three unique bands were sequenced from 12 DGGE profiles, excluding a composite fuzzy band of the Cytophaga-Flavobacterium group. The different methods gave similar distributions of taxa at the genus level and higher. However, the match at the species level among the methods was poor, and only one species was identified by all three methods. Consequently, all three methods identified unique subsets of bacterial species, amounting to a total richness of 97 operational taxonomic units in the experimental system. The confidence in the results was, however, dependent on the current precision of the phylogenetic determination and definition of the species. Bacterial consumers of RDOM in the studied estuary were primarily both cultivatable and uncultivable taxa of the Cytophaga-Flavobacterium group, a concordant result among the methods applied. Culture-independent methods also suggested several not-yet-cultivated beta-proteobacteria to be RDOM consumers.
|
|
| 9. |
- Kisand, Veljo, et al.
(author)
-
Genome sequencing of bacteria : sequencing, de novo assembly and rapid analysis using open source tools
- 2013
-
In: BMC Genomics. - : BIOMED CENTRAL LTD. - 1471-2164. ; 14
-
Journal article (peer-reviewed)abstract
- Background: De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads(<450 bps), which are presumed to aid in the analysis of uncharacterized genomes. The array of tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. Results: The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (similar to 30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Conclusions: Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize unknown bacteria with modest effort.
|
|
| 10. |
|
|
| 11. |
- Kisand, Veljo, et al.
(author)
-
Limited resolution of 16S rDNA DGGE caused by melting properties and closely related DNA sequences
- 2003
-
In: Journal of Microbiological Methods. - 0167-7012 .- 1872-8359. ; 54:2, s. 183-191
-
Journal article (peer-reviewed)abstract
- The phylogenetic affiliation of 91 operational taxonomic units, randomly sampled from three aquatic microcosm experiments, was investigated by two PCR based and one culture dependent method. The occurrence of multiple melting domains and poor coupling between Tin and DGGE retardation was demonstrated to cause poor resolution at the species level in PCR-DGGE analysis of microbial communities. We also showed that the problem of multiple melting domains was particularly prone for brackish water bacterioplankton in the Flavobacterium genus, providing characteristic band morphology for this genus. Banding patterns from DGGE analysis may therefore be misinterpreted in terms of the species richness in natural bacterial communities, when using commonly applied universal primers. (C) 2003 Elsevier Science B.V. All rights reserved.
|
|
| 12. |
- Kisand, Veljo, et al.
(author)
-
Phylogeny of culturable estuarine bacteria catabolizing riverine organic matter in the northern Baltic Sea
- 2002
-
In: Applied and Environmental Microbiology. - : American Society of Microbiology. - 0099-2240 .- 1098-5336. ; 68:1, s. 379-388
-
Journal article (peer-reviewed)abstract
- The objective of our study was to isolate and determine the phylogenetic affiliation of culturable estuarine bacteria capable of catabolizing riverine dissolved organic matter (RDOM) under laboratory conditions. Additions of RDOM consistently promoted the growth of estuarine bacteria in carbon-limited dilution cultures, with seasonal variation in growth rates and yields. At least 42 different taxa were culturable on solid agar media and, according to quantitative DNA-DNA hybridizations, constituted 32 to 89% of the total bacterial number in the enriched treatments. Five species in the Cytophaga-Flexibacter-Bacteroides group and one in the gamma-proteobacteria phylogenetic group (Marinomonas sp.) were numerically dominant during the stationary phase of the RDOM-enriched dilution cultures but not in the control cultures. Four of the isolates in Cytophaga-Flexibacter-Bacteroides group were putatively affiliated with the genus Flavobacterium. All dominating isolates were determined to be new species based on comparison to the current databases. The same group of species dominated independently of the season investigated, suggesting a low diversity of bacteria catabolizing RDOM in the estuary. It also suggested a broad tolerance of the dominating species to seasonal variation in hydrography, chemistry, and competition with other species. Taken together, our results suggest that a limited group of bacteria, mainly in the Flavobacterium genus, played an important role in introducing new energy and carbon to the marine system in the northern Baltic Sea.
|
|
| 13. |
- Kisand, Veljo, et al.
(author)
-
Prediction of COVID-19 positive cases, a nation-wide SARS-CoV-2 wastewater-based epidemiology study
- 2023
-
In: Water Research. - : Elsevier BV. - 1879-2448 .- 0043-1354. ; 231
-
Journal article (peer-reviewed)abstract
- Taking advantage of Estonia's small size and population, we have employed wastewater-based epidemiology approach to monitor the spread of SARS-CoV-2, releasing weekly nation-wide updates. In this study we report results obtained between August 2020 and December 2021. Weekly 24 h composite samples were collected from wastewater treatment plants of larger towns already covered 65% of the total population that was complemented up to 40 additional grab samples from smaller towns/villages and the specific sites of concern. The N3 gene abundance was quantified by RT-qPCR. The N3 gene copy number (concentration) in wastewater fluctuated in accordance with the SARS-CoV-2 spread within the total population, with N3 abundance starting to increase 1.25 weeks (9 days) (95% CI: [1.10, 1.41]) before a rise in COVID-19 positive cases. Statistical model between the load of virus in wastewater and number of infected people validated with the Alpha variant wave (B.1.1.17) could be used to predict the order of magnitude in incidence numbers in Delta wave (B.1.617.2) in fall 2021. Targeted testing of student dormitories, retirement and nursing homes and prisons resulted in successful early discovery of outbreaks. We put forward a SARS-CoV-2 Wastewater Index (SARS2-WI) indicator of normalized virus load as COVID-19 infection metric to complement the other metrics currently used in disease control and prevention: dynamics of effective reproduction number (Re), 7-day mean of new cases, and a sum of new cases within last 14 days. In conclusion, an efficient surveillance system that combines analysis of composite and grab samples was established in Estonia. There is considerable discussion how the viral load in wastewater correlates with the number of infected people. Here we show that this correlation can be found. Moreover, we confirm that an increased signal in wastewater is observed before the increase in the number of infections. The surveillance system helped to inform public health policy and place direct interventions during the COVID-19 pandemic in Estonia via early warning of epidemic spread in various regions of the country.
|
|
| 14. |
- Langenheder, Silke, et al.
(author)
-
Growth dynamics within bacterial communities in riverine and estuarine batch cultures
- 2004
-
In: Aquatic Microbial Ecology. - : Inter-Research Science Center. - 0948-3055 .- 1616-1564. ; 37, s. 137-148
-
Journal article (peer-reviewed)abstract
- We investigated temporal changes in community composition of bacteria growing on riverine dissolved organic carbon. Batch cultures were adjusted to riverine or estuarine salinity levels and inoculated with bacteria from these 2 environments to test whether growth patterns of bacterial taxa are influenced by salinity and/or the source of the inoculum. Changes in bacterial community composition at different stages of the growth phase were studied by 16S rDNA denaturing gradient gel electrophoresis (DGGE). Furthermore, the growth dynamics of 7 bacteria previously isolated from the estuary were followed by quantitative DNA-DNA hybridization. Growth dynamics within bacterial communities were significantly influenced by the source of the inoculum but not by salinity, suggesting that slight changes in salinity, to which riverine bacteria are exposed when discharged into the Northern Baltic Sea, are not a major regulating factor of community dynamics. Additionally, our results indicated only minor differences in the appearance and growth of bacteria when examined by quantitative DNA-DNA hybridization, whereas DGGE banding patterns suggested that there were fast- and slow-growing types of bacteria.
|
|
| 15. |
- Langenheder, Silke, et al.
(author)
-
Salinity as a structuring factor for the composition and performance of bacterioplankton degrading riverine DOC
- 2003
-
In: FEMS Microbiology Ecology. - 0168-6496 .- 1574-6941. ; 45:2, s. 189-202
-
Journal article (peer-reviewed)abstract
- The impact of salinity on the composition and functional performance (biomass production, growth efficiency and growth rates) of bacterial communities was investigated using batch cultures growing on dissolved organic carbon from a river draining into the Northern Baltic Sea. The cultures were adjusted to riverine or estuarine salinity levels and inoculated with bacteria from these two environments. Bacterial growth efficiencies differed in response to salinity and the origin of the inoculum. When salinity was adjusted to correspond to the salinity at the site where the inoculum was retrieved, growth efficiency was relatively high (11.5 +/- 2.6%). However, when bacteria were confronted with a shift in salinity, growth efficiency was lower (7.5 +/- 2.0%) and more of the utilized carbon was respired. In contrast, growth rates were higher when bacteria were exposed to a change in salinity. The composition of the bacterial communities developing in the batch cultures differed, as shown by 16S rDNA DGGE, depending on the origin of the inoculum and salinity. Reverse and direct DNA-DNA hybridization revealed salinity optima in the growth of specific bacterial strains as well as broader phylogenetic groups. Strains belonging to the alpha- and beta-Proteobacteria, Actinobacteria and gamma-Proteobacteria other than the genus Pseudomonas showed higher relative abundance under freshwater conditions, whereas strains of the genus Pseudomonas and the Cytophaga-Flavobacterium-Bacteroides group were favored by estuarine conditions. Generally, our results demonstrate functional changes associated with changes in community composition. We suggest that even moderate changes in salinity affect bacterial community composition, which subsequently leads to altered growth characteristics. (C) 2003 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
|
|
| 16. |
|
|
| 17. |
- Markussen, Trine, et al.
(author)
-
Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change
- 2018
-
In: Environmental Microbiology. - : Wiley-VCH Verlagsgesellschaft. - 1462-2912 .- 1462-2920. ; 20:8, s. 3083-3099
-
Journal article (peer-reviewed)abstract
- Bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes in marine environments, yet how bacterial communities respond to environmental change is not well known. Metagenomes allow examination of genetic responses of the entire microbial community to environmental change. However, it is challenging to link metagenomes directly to biogeochemical process rates. Here, we investigate metagenomic responses in natural bacterioplankton communities to simulated environmental stressors in the Baltic Sea, including increased river water input, increased nutrient concentration, and reduced oxygen level. This allowed us to identify informative prokaryotic gene markers, responding to environmental perturbation. Our results demonstrate that metagenomic and metabolic changes in bacterial communities in response to environmental stressors are influenced both by the initial community composition and by the biogeochemical factors shaping the functional response. Furthermore, the different sources of dissolved organic matter (DOM) had the largest impact on metagenomic blueprint. Most prominently, changes in DOM loads influenced specific transporter types reflecting the substrate availability and DOC assimilation and consumption pathways. The results provide new knowledge for developing models of ecosystem structure and biogeochemical cycling in future climate change scenarios and advance our exploration of the potential use of marine microorganisms as markers for environmental conditions.
|
|
| 18. |
- Osbeck, Christofer M. G., et al.
(author)
-
Divergent transcriptional responses of Baltic Sea bacteria to forest and agriculture river loadings
-
Other publication (other academic/artistic)abstract
- Climate change is projected to induce substantial changes in precipitation patterns across the globe. In Northern Europe, precipitation is expected to increase more than the global average (particularly in northern Scandinavia), causing increased river runoff. The Baltic Sea is one of the largest brackish environments on earth with a catchment area that spans 14 countries, encompassing primarily forested areas and agricultural landscapes. Despite the acknowledged role of marine bacteria in nutrient cycling, there is a lack of knowledge in their metabolic responses to inorganic and organic nutrient loading from riverine runoff. We investigated the bacterial growth and gene expression responses in a mesocosm experiment in which river water from boreal forest- (enriched in humic substances) or agriculture-influenced catchment areas (enriched in nitrogen) were added to Baltic Proper water. The riverine nutrient input triggered extensive phytoplankton blooms and bacterial growth, most notably in the agriculture river treatment. Interestingly, bacterial gene expression analysis (metatranscriptomics) showed similar responses to agriculture and humic river inputs at the start of the experiment during phytoplankton development, but expression patterns diverged upon bloom senescence. This indicated that interactions between river nutrient loading and phytoplankton organic matter are important in regulating bacterial activities and responses at the molecular level. Notably, transcripts associated with phosphate metabolism were significantly enriched in the agriculture river treatment compared to the boreal forest river treatment, whereas transcripts related to nitrogen metabolism were significantly lower. The opposite pattern was observed in the boreal forest river water treatment. This suggests that bacterial transformations of organic matter and nutrient processing in coastal environments are sensitive to alterations in the precipitation-induced riverine runoff in a catchment area-dependent manner, which has implications for interpreting the ecosystem effects of globally changing precipitation patterns.
|
|
| 19. |
- Tedersoo, Leho, et al.
(author)
-
Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi
- 2015
-
In: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 10, s. 1-43
-
Journal article (peer-reviewed)abstract
- Rapid development of high-throughput (HTS) molecular identification methods has revolutionized our knowledge about taxonomic diversity and ecology of fungi. However, PCR-based methods exhibit multiple technical shortcomings that may bias our understanding of the fungal kingdom. This study was initiated to quantify potential biases in fungal community ecology by comparing the relative performance of amplicon-free shotgun metagenomics and amplicons of nine primer pairs over seven nuclear ribosomal DNA (rDNA) regions often used in metabarcoding analyses. The internal transcribed spacer (ITS) barcodes ITS1 and ITS2 provided greater taxonomic and functional resolution and richness of operational taxonomic units (OTUs) at the 97% similarity threshold compared to barcodes located within the ribosomal small subunit (SSU) and large subunit (LSU) genes. All barcode-primer pair combinations provided consistent results in ranking taxonomic richness and recovering the importance of floristic variables in driving fungal community composition in soils of Papua New Guinea. The choice of forward primer explained up to 2.0% of the variation in OTU-level analysis of the ITS1 and ITS2 barcode data sets. Across the whole data set, barcode-primer pair combination explained 37.6–38.1% of the variation, which surpassed any environmental signal. Overall, the metagenomics data set recovered a similar taxonomic overview, but resulted in much lower fungal rDNA sequencing depth, inability to infer OTUs, and high uncertainty in identification. We recommend the use of ITS2 or the whole ITS region for metabarcoding and we advocate careful choice of primer pairs in consideration of the relative proportion of fungal DNA and expected dominant groups.
|
|
| 20. |
- Wikner, Johan, 1961-, et al.
(author)
-
Coastal filter effect by microbial mineralization of riverine DOC in a sub-arctic river-estuary gradient
-
Other publication (other academic/artistic)abstract
- The existence of a coastal filtering effect was studied in a 16 km boreal river-estuary system (RES) during contrasting low and high production conditions. Marked transformations occurred within 5 km (salinity 3) from the river mouth for many of the variables during high productive conditions. During the less productive season changes were small and occurred closer to the river mouth. Active transformation dominated the patterns detected in August (53 %), while mixing of river and coastal marine water was the dominant process in April. Bacterial community respiration was similar during both seasons averaging 2.6 μmol O2 dm-3 d-1, indicating efficient remineralization of riverine dissolved organic carbon (DOC). This was further reflected in a low and variable bacterial growth efficiency (BGE) with a mean of 12 % in the surface water at high productivity, but only 3 % at low productivity conditions. Bacterial community growth (BCG) showed strong relationship to water temperature at both seasons indicating energy limitation. Some indication of removal of nitrogen was observed, while no removal of phosphorus could be demonstrated. Phosphorus concentration showed a strong reciprocal power-function relationship to BCG, suggesting efficient assimilation of the limiting nutrient at carbon sufficiency. Marked spatial changes in diversity of phytoplankton, protozoa and bacterioplankton occurred at low salinities within 1 km from the river mouth. We conclude that this subarctic estuary acts as a coastal filter mainly by remineralizing riverine DOC to CO2.
|
|
