{"entity": "journal", "iuid": "5651c2cddfef4655abf7b0a713c5fa5f", "timestamp": "2026-07-20T00:37:35.118Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/J%20Environ%20Manage.json"}, "display": {"href": "https://publications.scilifelab.se/journal/J%20Environ%20Manage"}}, "title": "J Environ Manage", "issn": "1095-8630", "issn-l": null, "publications_count": 5, "publications": [{"entity": "publication", "iuid": "e43fd2012d994dabbae3508be896f740", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e43fd2012d994dabbae3508be896f740.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e43fd2012d994dabbae3508be896f740"}}, "title": "Genome-centric metagenomics reveals the effect of organic carbon source on one-stage partial denitrification-anammox in biofilm reactors.", "authors": [{"family": "Zheng", "given": "Zejia", "initials": "Z"}, {"family": "Gustavsson", "given": "David J I", "initials": "DJI"}, {"family": "Zheng", "given": "Dan", "initials": "D"}, {"family": "Holmin", "given": "Felix", "initials": "F"}, {"family": "Fal\u00e5s", "given": "Per", "initials": "P"}, {"family": "Wil\u00e9n", "given": "Britt-Marie", "initials": "BM"}, {"family": "Modin", "given": "Oskar", "initials": "O"}, {"family": "Persson", "given": "Frank", "initials": "F"}], "type": "journal article", "published": "2025-07-00", "journal": {"title": "J Environ Manage", "issn": "1095-8630", "volume": "388", "pages": "125972", "issn-l": null}, "abstract": "Nitrogen removal from wastewater with anammox saves energy and resources. Partial denitrification-anammox (PDA) is a promising process alternative for municipal wastewater treatment, given that the understanding about how to control the microbiome and its activity reach sufficient level. Here, two moving bed biofilm reactors were fed with either acetate or propionate to study the role of organic carbon type for microbiome composition and nitrogen turnover during development of PDA. With acetate, 87 % of the removed nitrogen was converted via anammox during stable operation at a rate of 0.52 g N/(m2\u00b7d). With propionate, the anammox contribution was considerably lower (41 %), as was the rate of nitrogen removal (0.27 g N/(m2\u00b7d)). The microbiome composition in the acetate- and propionate-fed reactors was however similar, with an enrichment of metagenome assembled genomes (MAGs) having genes for nitrate reduction (narG, napA). A large fraction of these MAGs had the potential to accumulate nitrite since they lacked genes for nitrite reduction (nirS, nirK, nrfA). Genes for acetate utilization were common among these MAGs, but the necessary genes for propionate conversion were rare, suggesting that the genetic make-up of the individual denitrifiers had major influence on the nitrogen turnover. One anammox MAG (Ca. Brocadia sapporoensis), harboring genes for organic carbon utilization, prevailed in the PDA reactors. Another three anammox MAGs (Ca. B. fulgida, Ca. B. pituitae and a potentially new species within Ca. Brocadia), lacking genes for organic carbon utilization, decreased in abundance in the reactors, indicating the importance of metabolic versatility for anammox bacteria in PDA.", "doi": "10.1016/j.jenvman.2025.125972", "pmid": "40449445", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0301-4797(25)01948-6"}], "notes": [], "created": "2025-11-28T10:44:00.290Z", "modified": "2025-11-28T10:44:00.301Z"}, {"entity": "publication", "iuid": "dd55ea22434a4496a1f1fd1dfc7f0e75", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dd55ea22434a4496a1f1fd1dfc7f0e75.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dd55ea22434a4496a1f1fd1dfc7f0e75"}}, "title": "Effects of livestock on arthropod biodiversity in Iberian holm oak savannas revealed by metabarcoding.", "authors": [{"family": "Canelo", "given": "Tara", "initials": "T"}, {"family": "Marquina", "given": "Daniel", "initials": "D"}, {"family": "Chozas", "given": "Sergio", "initials": "S"}, {"family": "Bergsten", "given": "Johannes", "initials": "J"}, {"family": "Gayt\u00e1n", "given": "\u00c1lvaro", "initials": "\u00c1"}, {"family": "P\u00e9rez-Izquierdo", "given": "Carlos", "initials": "C"}, {"family": "Bonal", "given": "Ra\u00fal", "initials": "R"}], "type": "journal article", "published": "2024-08-00", "journal": {"title": "J Environ Manage", "issn": "1095-8630", "volume": "365", "pages": "121619", "issn-l": null}, "abstract": "Increasing food production while avoiding negative impacts on biodiversity constitutes one of the main challenges of our time. Traditional silvopastoral systems like Iberian oak savannas (\"dehesas\") set an example, where free-range livestock has been reared for centuries while preserving a high natural value. Nevertheless, factors decreasing productivity need to be addressed, one being acorn losses provoked by pest insects. An increased and focalized grazing by livestock on infested acorns would kill the larvae inside and decrease pest numbers, but increased livestock densities could have undesired side effects on ground arthropod communities as a whole. We designed an experimental setup including areas under trees with livestock exclosures of different ages (short-term: 1-year exclusion, long-term: 10-year exclusion), along with controls (continuous grazing), using DNA metabarcoding (mitochondrial markers COI and 16S) to rapidly assess arthropod communities' composition. Livestock removal quickly increased grass cover and arthropod taxonomic richness and diversity, which was already higher in short-term (1-year exclosures) than beneath the canopies of control trees. Interestingly, arthropod diversity was not highest at long-term exclosures (\u226510 years), although their community composition was the most distinct. Also, regardless of treatment, we found that functional diversity strongly correlated with the vegetation structure, being higher at trees beneath which there was higher grass cover and taller herbs. Overall, the taxonomic diversity peak at short term exclosures would support the intermediate disturbance hypothesis, which relates it with the higher microhabitat heterogeneity at moderately disturbed areas. Thus, we propose a rotatory livestock management in dehesas: plots with increased grazing should co-exist with temporal short-term exclosures. Ideally, a few long-term excluded areas should be also kept for the singularity of their arthropod communities. This strategy would make possible the combination of biological pest control and arthropod conservation in Iberian dehesas.", "doi": "10.1016/j.jenvman.2024.121619", "pmid": "38963962", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0301-4797(24)01605-0"}], "notes": [], "created": "2025-02-28T14:12:26.644Z", "modified": "2025-02-28T14:12:26.649Z"}, {"entity": "publication", "iuid": "433fbcdbe4af4353acf3eda9ea1ddc67", "links": {"self": {"href": "https://publications.scilifelab.se/publication/433fbcdbe4af4353acf3eda9ea1ddc67.json"}, "display": {"href": "https://publications.scilifelab.se/publication/433fbcdbe4af4353acf3eda9ea1ddc67"}}, "title": "Microbial succession and denitrifying woodchip bioreactor performance at low water temperatures.", "authors": [{"family": "Hellman", "given": "Maria", "initials": "M"}, {"family": "Juhanson", "given": "Jaanis", "initials": "J"}, {"family": "Walln\u00e4s", "given": "Felicia", "initials": "F"}, {"family": "Herbert", "given": "Roger B", "initials": "RB"}, {"family": "Hallin", "given": "Sara", "initials": "S"}], "type": "journal article", "published": "2024-04-00", "journal": {"title": "J Environ Manage", "issn": "1095-8630", "volume": "356", "pages": "120607", "issn-l": null}, "abstract": "Mining activities are increasingly recognized for contributing to nitrogen (N) pollution and possibly also to emissions of the greenhouse gas nitrous oxide (N2O) due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities, including the genetic potential for different N transformation processes, in pore water and woodchips and how this related to reactor N removal capacity. About 80 and 65 % of the nitrate was removed during the first and second operational year, respectively. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in reactor performance. Nitrate ammonification likely had minimal impact on N removal efficiency due to the low production of ammonium and low abundance of the key gene nrfA in ammonifiers. Nitrite and N2O were formed in the bioreactor and released in the effluent water, although direct N2O emissions from the surface was low. That these unwanted reactive N species were produced at different times and locations in the reactor indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length. We conclude that the succession of microbial communities in woodchip denitrifying bioreactors treating mining water develops slowly at low temperature, which impacts reactor performance.", "doi": "10.1016/j.jenvman.2024.120607", "pmid": "38537471", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "S0301-4797(24)00593-0"}], "notes": [], "created": "2024-05-16T06:31:09.458Z", "modified": "2024-05-16T06:31:09.461Z"}, {"entity": "publication", "iuid": "15dd8ce54a0942f595d26e915274968e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15dd8ce54a0942f595d26e915274968e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15dd8ce54a0942f595d26e915274968e"}}, "title": "The effects of pH on the production of volatile fatty acids and microbial dynamics in long-term reactor operation.", "authors": [{"family": "Atasoy", "given": "Merve", "initials": "M"}, {"family": "Cetecioglu", "given": "Zeynep", "initials": "Z"}], "type": "journal article", "published": "2022-10-01", "journal": {"title": "J Environ Manage", "issn": "1095-8630", "volume": "319", "pages": "115700", "issn-l": null}, "abstract": "Volatile fatty acids, intermediate products of anaerobic digestion, are one of the most promising biobased products. In this study, the effects of acidic (pH 5), neutral (without pH adjustment) and alkali (pH 10) pH on production efficiency and composition of volatile fatty acids (VFAs) and bacterial community profile were analyzed. The anaerobic sequencing batch reactors were fed cheese production wastewater as substrate and inoculated by anaerobic granular seed sludge. The results showed that acidic pH improved VFA production yield (0.92 at pH 5; 0.42 at pH 10 and 0.21 gCOD/gVS at neutral pH). Furthermore, propionic acid was dominant under both pH 10 (64 \u00b1 20%) and neutral pH (72 \u00b1 8%), whereas, acetic acid (23 \u00b1 20%4), propionic acid (22 \u00b1 3%), butyric acid (21 \u00b1 4%) and valeric acid (15 \u00b1 8%) were almost equally distributed under pH 5. Adaptation of bacterial community to different pH conditions might steer the acid profile: Bacteroidetes (50.07 \u00b1 2%) under pH 10, Proteobacteria (40.74 \u00b1 7%) under neutral pH and Firmicutes (47.64 \u00b1 9%) under pH 5 were the most dominant phylum, respectively. Results indicated pH plays a significant role in VFA production, acid composition, and bacterial community structure. However, in order to gain a concrete understanding effects of pH, characterization of intracellular and extracellular metabolites with dynamics of the microbial community is required.", "doi": "10.1016/j.jenvman.2022.115700", "pmid": "35982552", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0301-4797(22)01273-7"}], "notes": [], "created": "2022-11-09T15:45:16.511Z", "modified": "2024-01-16T13:48:34.810Z"}, {"entity": "publication", "iuid": "d7b2754d3b5344eca206a9db987efa4f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7b2754d3b5344eca206a9db987efa4f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7b2754d3b5344eca206a9db987efa4f"}}, "title": "Bioaugmentation as a strategy for tailor-made volatile fatty acid production.", "authors": [{"family": "Atasoy", "given": "Merve", "initials": "M"}, {"family": "Cetecioglu", "given": "Zeynep", "initials": "Z"}], "type": "journal article", "published": "2021-10-01", "journal": {"title": "J Environ Manage", "issn": "1095-8630", "volume": "295", "pages": "113093", "issn-l": null}, "abstract": "This study aimed to develop a novel strategy for tailor-made volatile fatty acid (VFA) composition. For this purpose, the mixed microbial culture was bioaugmented by Propionibacterium acidipropionici. Anaerobic sequencing batch reactors were operated with cheese wastewater under alkali pH. While the maximum propionic acid production almost four times increased (3779 \u00b1 201 mgCODeq propionic acid/L in the bioaugmented reactor and 942 \u00b1 172 mgCODeq propionic acid/L in the control reactor), there was no significant difference in VFA composition. The gene copy number of P.acidipropionici increased 20 times after the bioaugmentation. Furthermore, the gene copy number of P.acidipropionici was positively correlated with total VFA and isovaleric acid concentration. The relative abundance of family Flavobacteriaceae increased in the bioaugmented reactor, which might be caused by the syntrophic relation between Flavobacteriaceae and P. acidipropionici. The cycle analysis results showed that the shorter cycle (6h) could ensure the same efficiency.", "doi": "10.1016/j.jenvman.2021.113093", "pmid": "34167052", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "S0301-4797(21)01155-5"}], "notes": [], "created": "2022-11-09T15:46:10.270Z", "modified": "2024-01-16T13:48:38.318Z"}], "created": "2022-11-09T15:45:16.517Z", "modified": "2022-11-09T15:45:16.517Z"}