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Martella, G., Motwani, N. H., Khan, Z., Sousa, P. F. M., Gorokhova, E. & Motwani, H. V. (2023). Simultaneous RNA and DNA Adductomics Using Single Data-Independent Acquisition Mass Spectrometry Analysis. Chemical Research in Toxicology, 36(9), 1471-1482
Open this publication in new window or tab >>Simultaneous RNA and DNA Adductomics Using Single Data-Independent Acquisition Mass Spectrometry Analysis
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2023 (English)In: Chemical Research in Toxicology, ISSN 0893-228X, E-ISSN 1520-5010, Vol. 36, no 9, p. 1471-1482Article in journal (Refereed) Published
Abstract [en]

Adductomics studies are used for the detection and characterization of various chemical modifications (adducts) of nucleic acids and proteins. The advancements in liquid chromatography coupled with high-resolution tandem mass spectrometry (HRMS/MS) have resulted in efficient methods for qualitative and quantitative adductomics. We developed an HRMS-based method for the simultaneous analysis of RNA and DNA adducts in a single run and demonstrated its application using Baltic amphipods, useful sentinels of environmental disturbances, as test organisms. The novelty of this method is screening for RNA and DNA adducts by a single injection on an Orbitrap HRMS instrument using full scan and data-independent acquisition. The MS raw files were processed with an open-source program, nLossFinder, to identify and distinguish RNA and DNA adducts based on the characteristic neutral loss of ribonucleosides and 2'-deoxyribonucleosides, respectively. In the amphipods, in addition to the nearly 150 putative DNA adducts characterized earlier, we detected 60 putative RNA adducts. For the structural identification of the detected RNA adducts, the MODOMICS database was used. The identified RNA adducts included simple mono- and dimethylation and other larger functional groups on different ribonucleosides and deaminated product inosine. However, 54 of these RNA adducts are not yet structurally identified, and further work on their characterization may uncover new layers of information related to the transcriptome and help understand their biological significance. Considering the susceptibility of nucleic acids to environmental factors, including pollutants, the developed multi-adductomics methodology with further advancement has the potential to provide biomarkers for diagnostics of pollution effects in biota.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2023
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:sh:diva-52227 (URN)10.1021/acs.chemrestox.3c00041 (DOI)001047857700001 ()37566384 (PubMedID)2-s2.0-85169329956 (Scopus ID)
Funder
Swedish Research Council Formas, 2019-01157The Foundation for Baltic and East European Studies, 56/19
Available from: 2023-08-29 Created: 2023-08-29 Last updated: 2023-09-27Bibliographically approved
Garrison, J. A., Motwani, N. H., Broman, E. & Nascimento, F. J. A. (2022). Molecular diet analysis enables detection of diatom and cyanobacteria DNA in the gut of Macoma balthica. PLOS ONE, 17(11), Article ID e0278070.
Open this publication in new window or tab >>Molecular diet analysis enables detection of diatom and cyanobacteria DNA in the gut of Macoma balthica
2022 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 17, no 11, article id e0278070Article in journal (Refereed) Published
Abstract [en]

Detritivores are essential to nutrient cycling, but are often neglected in trophic networks, due to difficulties with determining their diet. DNA analysis of gut contents shows promise of trophic link discrimination, but many unknown factors limit its usefulness. For example, DNA can be rapidly broken down, especially by digestion processes, and DNA provides only a snapshot of the gut contents at a specific time. Few studies have been performed on the length of time that prey DNA can be detected in consumer guts, and none so far using benthic detritivores. Eutrophication, along with climate change, is altering the phytoplankton communities in aquatic ecosystems, on which benthic detritivores in aphotic soft sediments depend. Nutrient-poor cyanobacteria blooms are increasing in frequency, duration, and magnitude in many water bodies, while nutrient-rich diatom spring blooms are shrinking in duration and magnitude, creating potential changes in diet of benthic detritivores. We performed an experiment to identify the taxonomy and quantify the abundance of phytoplankton DNA fragments on bivalve gut contents, and how long these fragments can be detected after consumption in the Baltic Sea clam Macoma balthica. Two common species of phytoplankton (the cyanobacteria Nodularia spumigena or the diatom Skeletonema marinoi) were fed to M. balthica from two regions (from the northern and southern Stockholm archipelago). After removing the food source, M. balthica gut contents were sampled every 24 hours for seven days to determine the number of 23S rRNA phytoplankton DNA copies and when the phytoplankton DNA could no longer be detected by quantitative PCR. We found no differences in diatom 18S rRNA gene fragments of the clams by region, but the southern clams showed significantly more cyanobacteria 16S rRNA gene fragments in their guts than the northern clams. Interestingly, the cyanobacteria and diatom DNA fragments were still detectable by qPCR in the guts of M. balthica one week after removal from its food source. However, DNA metabarcoding of the 23S rRNA phytoplankton gene found in the clam guts showed that added food (i.e. N. spumigena and S. marinoi) did not make up a majority of the detected diet. Our results suggest that these detritivorous clams therefore do not react as quickly as previously thought to fresh organic matter inputs, with other phytoplankton than large diatoms and cyanobacteria constituting the majority of their diet. This experiment demonstrates the viability of using molecular methods to determine feeding of detritivores, but further studies investigating how prey DNA signals can change over time in benthic detritivores will be needed before this method can be widely applicable to both models of ecological functions and conservation policy.

Place, publisher, year, edition, pages
Public Library of Science, 2022
National Category
Biochemistry and Molecular Biology
Research subject
Baltic and East European studies
Identifiers
urn:nbn:se:sh:diva-50304 (URN)10.1371/journal.pone.0278070 (DOI)000925653100064 ()36417463 (PubMedID)2-s2.0-85142935095 (Scopus ID)
Funder
Swedish Environmental Protection Agency, NV-802-0151-18The Foundation for Baltic and East European Studies, 56/19
Available from: 2022-11-29 Created: 2022-11-29 Last updated: 2023-06-01Bibliographically approved
Albert, S., Hedberg, P., Motwani, N. H., Sjöling, S., Winder, M. & Nascimento, F. J. (2021). Phytoplankton settling quality has a subtle but significant effect on sediment microeukaryotic and bacterial communities. Scientific Reports, 11(1), Article ID 24033.
Open this publication in new window or tab >>Phytoplankton settling quality has a subtle but significant effect on sediment microeukaryotic and bacterial communities
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2021 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 11, no 1, article id 24033Article in journal (Refereed) Published
Abstract [en]

In coastal aphotic sediments, organic matter (OM) input from phytoplankton is the primary food resource for benthic organisms. Current observations from temperate ecosystems like the Baltic Sea report a decline in spring bloom diatoms, while summer cyanobacteria blooms are becoming more frequent and intense. These climate-driven changes in phytoplankton communities may in turn have important consequences for benthic biodiversity and ecosystem functions, but such questions are not yet sufficiently explored experimentally. Here, in a 4-week experiment, we investigated the response of microeukaryotic and bacterial communities to different types of OM inputs comprising five ratios of two common phytoplankton species in the Baltic Sea, the diatom Skeletonema marinoi and filamentous cyanobacterium Nodularia spumigena. Metabarcoding analyses on 16S and 18S ribosomal RNA (rRNA) at the experiment termination revealed subtle but significant changes in diversity and community composition of microeukaryotes in response to settling OM quality. Sediment bacteria were less affected, although we observed a clear effect on denitrification gene expression (nirS and nosZ), which was positively correlated with increasing proportions of cyanobacteria. Altogether, these results suggest that future changes in OM input to the seafloor may have important effects on both the composition and function of microbenthic communities.

Place, publisher, year, edition, pages
Springer Nature, 2021
National Category
Ecology
Research subject
Environmental Studies; Baltic and East European studies
Identifiers
urn:nbn:se:sh:diva-47894 (URN)10.1038/s41598-021-03303-x (DOI)000730739800052 ()34911983 (PubMedID)2-s2.0-85121378825 (Scopus ID)
Funder
Swedish Research Council Formas, 2016-00804Swedish Research Council Formas, 2015-1320The Foundation for Baltic and East European Studies, 77/2017
Available from: 2021-12-21 Created: 2021-12-21 Last updated: 2022-09-15Bibliographically approved
Gorokhova, E., Soerensen, A. L. & Motwani, N. H. (2020). Mercury-methylating bacteria are associated with copepods: A proof-of-principle survey in the Baltic Sea. PLOS ONE, 15(3), Article ID e0230310.
Open this publication in new window or tab >>Mercury-methylating bacteria are associated with copepods: A proof-of-principle survey in the Baltic Sea
2020 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 15, no 3, article id e0230310Article in journal (Refereed) Published
Abstract [en]

Methylmercury (MeHg) is a potent neurotoxin that biomagnifies in marine food webs. Inorganic mercury (Hg) methylation is conducted by heterotrophic bacteria inhabiting sediment or settling detritus, but endogenous methylation by the gut microbiome of animals in the lower food webs is another possible source. We examined the occurrence of the bacterial gene (hgcA), required for Hg methylation, in the guts of dominant zooplankters in the Northern Baltic Sea. A qPCR assay targeting the hgcA sequence in three main clades (Deltaproteobacteria, Firmicutes and Archaea) was used in the field-collected specimens of copepods (Acartia bifilosa, Eurytemora affinis, Pseudocalanus acuspes and Limnocalanus macrurus) and cladocerans (Bosmina coregoni maritima and Cercopagis pengoi). All copepods were found to carry hgcA genes in their gut microbiome, whereas no amplification was recorded in the cladocerans. In the copepods, hgcA genes belonging to only Deltaproteobacteria and Firmicutes were detected. These findings suggest a possibility that endogenous Hg methylation occurs in zooplankton and may contribute to seasonal, spatial and vertical MeHg variability in the water column and food webs. Additional molecular and metagenomics studies are needed to identify bacteria carrying hgcA genes and improve their quantification in microbiota.

Place, publisher, year, edition, pages
Public Library of Science, 2020
National Category
Environmental Sciences
Research subject
Baltic and East European studies
Identifiers
urn:nbn:se:sh:diva-40421 (URN)10.1371/journal.pone.0230310 (DOI)000535291800026 ()32176728 (PubMedID)2-s2.0-85081963074 (Scopus ID)
Funder
Swedish Research Council, 2018- 05213Swedish Research Council Formas, 2018- 01010
Available from: 2020-03-24 Created: 2020-03-24 Last updated: 2021-06-14Bibliographically approved
Broman, E., Motwani, N. H., Bonaglia, S., Landberg, T., Nascimento, F. J. & Sjöling, S. (2019). Denitrification responses to increasing cadmium exposure in Baltic Sea sediments. Aquatic Toxicology, 217, Article ID 105328.
Open this publication in new window or tab >>Denitrification responses to increasing cadmium exposure in Baltic Sea sediments
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2019 (English)In: Aquatic Toxicology, ISSN 0166-445X, E-ISSN 1879-1514, Vol. 217, article id 105328Article in journal (Refereed) Published
Abstract [en]

Benthic ecosystems have come under intense pressure, due to eutrophication-driven oxygen decline and industrial metal contamination. One of the most toxic metals is Cadmium (Cd), which is lethal to many aquatic organisms already at low concentrations. Denitrification by facultative anaerobic microorganisms is an essential process to transform, but also to remove, excess nitrate in eutrophied systems. Cd has been shown to decrease denitrification and sequester free sulfide, which is available when oxygen is scarce and generally inhibits complete denitrification (i.e. N2O to N2). In polluted sediments, an interaction between oxygen and Cd may influence denitrification and this relationship has not been studied. For example, in the Baltic Sea some sediments are double exposed to both Cd and hypoxia. In this study, we examined how the double exposure of Cd and fluctuations in oxygen affects denitrification in Baltic Sea sediment. Results show that oxygen largely regulated N2O and N2 production after 21 days of exposure to Cd (ranging from 0 to 500 μg/L, 5 different treatments, measured by the isotope pairing technique (IPT)). In the high Cd treatment (500 μg/L) the variation in N2 production increased compared to the other treatments. Increases in N2 production are suggested to be an effect of 1) enhanced nitrification that increases NO3 − availability thus stimulating denitrification, and 2) Cd successfully sequestrating sulfide (yielding CdS), which allows for full denitrification to N2. The in situ field sediment contained initially high Cd concentrations in the pore water (∼10 μg/L) and microbial communities might already have been adapted to metal stress, making the effect of low Cd levels negligible. Here we show that high levels of cadmium pollution might increase N2 production and influence nitrogen cycling in marine sediments. © 2019 The Authors

Place, publisher, year, edition, pages
Elsevier, 2019
Keywords
Baltic Sea, Benthos, Denitrification, Hypoxia, Oxygen, Pollution, Sediment
National Category
Environmental Sciences
Research subject
Environmental Studies; Baltic and East European studies
Identifiers
urn:nbn:se:sh:diva-39283 (URN)10.1016/j.aquatox.2019.105328 (DOI)000501413700002 ()31629202 (PubMedID)2-s2.0-85073170054 (Scopus ID)3150-3.1.1-2017 (Local ID)3150-3.1.1-2017 (Archive number)3150-3.1.1-2017 (OAI)
Funder
The Foundation for Baltic and East European Studies, 77/2017
Available from: 2019-10-31 Created: 2019-10-31 Last updated: 2023-06-01Bibliographically approved
Projects
Response and recovery of benthic biodiversity and ecosystem functions to chemical pollution and eutrophication [77/2017_OSS]; Södertörn University; Publications
Abdelgadir, M., Alharbi, R., AlRashidi, M., Alatawi, A. S., Sjöling, S. & Dinnétz, P. (2023). Distribution of denitrifiers predicted by correlative niche modeling of changing environmental conditions and future climatic scenarios across the Baltic Sea. Ecological Informatics, 78, Article ID 102346. Broman, E., Abdelgadir, M., Bonaglia, S., Forsberg, S. C., Wikström, J., Gunnarsson, J. S., . . . Sjöling, S. (2023). Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities. Microbial Ecology, 86, 2357-2372Albert, S., Hedberg, P., Motwani, N. H., Sjöling, S., Winder, M. & Nascimento, F. J. (2021). Phytoplankton settling quality has a subtle but significant effect on sediment microeukaryotic and bacterial communities. Scientific Reports, 11(1), Article ID 24033. Broman, E., Motwani, N. H., Bonaglia, S., Landberg, T., Nascimento, F. J. & Sjöling, S. (2019). Denitrification responses to increasing cadmium exposure in Baltic Sea sediments. Aquatic Toxicology, 217, Article ID 105328. Sommer, C., Hu, Y., Nascimento, F., Gunnarsson, J., Dinnétz, P. & Sjöling, S. (2019). Reduced large-scale beta-diversity and changes in metapopulation patterns of sediment bacterial communities following a major inflow into the Baltic Sea. Environmental MicrobiologySjöling, S., van Elsas, J. D., Andreote, F. D. & Rodrigues, J. L. (2019). Soil Metagenomics: deceiphering the soil microbial gene pool (3ed.). In: JD van Elsas, JT Trevors, As Rosado, P Nannipieri (Ed.), Modern Soil Microbiology: (pp. 227-243). Boca Raton: CRC Press
Bacteria-driven Hg methylation in microbiome of lower consumers [56/2019_OSS]; Södertörn University; Publications
Martella, G., Motwani, N. H., Khan, Z., Sousa, P. F. M., Gorokhova, E. & Motwani, H. V. (2023). Simultaneous RNA and DNA Adductomics Using Single Data-Independent Acquisition Mass Spectrometry Analysis. Chemical Research in Toxicology, 36(9), 1471-1482Garrison, J. A., Motwani, N. H., Broman, E. & Nascimento, F. J. A. (2022). Molecular diet analysis enables detection of diatom and cyanobacteria DNA in the gut of Macoma balthica. PLOS ONE, 17(11), Article ID e0278070.
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