Sanni L. Aalto

The unintended microbiological production of hydrogen sulphide (H ₂ S) poses a significant challenge in engineered systems, including sewage treatment plants, landfills and aquaculture systems. Although sulphur‐rich amino acids and other substrates conducive to non‐sulphate‐based H ₂ S production are frequently present, the capacity and potential of various microorganisms to perform sulphate‐free H ₂ S production remain unclear. In this study, we identify the identity, activity and genomic characteristics of bacteria that degrade cysteine to produce H ₂ S in anaerobic enrichment bioreactors seeded with material from aquaculture systems. Our comparison with canonical sulphate‐reducing bacteria reveals that both sulphur sources contribute to microbial H ₂ S production, with cysteine facilitating a more rapid process compared to sulphate. 16S rRNA amplicon sequencing and metagenomic analysis identified four bacterial families— Dethiosulfatibacteraceae , Fusobacteriaceae , Vibrionaceae and Desulfovibrionaceae —as central to non‐sulphate H ₂ S production. Metagenome‐ and metatranscriptome‐assembled genomes elucidated the primary cysteine degradation pathway mediated by cysteine desulphidase cyuA and indicated that some bacteria may also utilise cysteine as a carbon source in sulphate‐based H ₂ S production.

Unwanted microbiological production of hydrogen sulfide (H₂S) is a major challenge in engineered systems, such as sewage treatment plants, landfills, and aquaculture systems. While sulfur-rich amino acids and other substrates for non-sulfate-based H₂S production are commonly present, the ability and potential of different microorganisms to perform sulfate-free H₂S production has not yet been resolved. Here, we reveal the identity, activity, and genomic characteristics of bacteria that degrade cysteine to produce H₂S in anaerobic enrichment bioreactors seeded with material from aquaculture systems. We compared them with canonical sulfate reducing bacteria and found that both sulfur sources led to microbial H₂S production, yet with the process being more rapid with cysteine than with sulfate. 16S rRNA amplicon sequencing and metagenomic analysis showed four bacterial families, Dethiosulfatibacteraceae, Fusobacteriaceae, Vibrionaceae, and Desulfovibrionaceae to be centrally involved in non-sulfate H₂S production. Metagenome/metatranscriptome assembled genomes uncovered the main cysteine-degradation pathway mediated by cysteine desulfidase cyuA and revealed that some bacteria potentially also use cysteine as a carbon source in sulfate-based H₂S production. Our findings call for a revised view of microbial H₂S production in engineered systems.

The successful establishment of European lobster (Homarus gammarus) land-based production is hampered by the high mortality rate during larval development, which can be partially explained by the proliferation of pathogens in the communal tanks commonly used for larval rearing. Therefore, disinfection water treatment could improve the low survival rates frequently recorded in H. gammarus farming. In this study, we evaluated the effect of UV irradiation on the microbial abundance and physicochemical quality of the culture water, as well as on H. gammarus larvae growth and survival reared on a flow-through system for a period of 15 days. Results showed that UV treatment significantly decreased the microbial abundance and reduced the variation in water parameters but did not improve physicochemical water quality (turbidity, ultraviolet transmission, nitrogenous compounds, biochemical, and chemical oxygen demand). Moreover, contrary to the expectations, UV irradiation did not improve but slowed down larvae growth. We initially hypothesized that UV disinfection would enhance the rearing water quality by inactivating bacteria, including potential pathogens, and hence, benefit larvae growth and survival. Our findings suggest that UV disinfection can stabilize the rearing environment but does not benefit H. gammarus larvae rearing, at least in a flow-through system set-up. This could be due to UV disinfection eliminating not only potential harmful pathogens but also other microbial groups important for the establishment of a healthy gut microbiota supporting lobster larvae growth.

The identity of electron acceptors in promoting anaerobic oxidation of methane (AOM) in the sediments of boreal lakes is currently unknown. Here, we studied the AOM rate of sediment slurries collected from three profundal stations of a nitrate-rich, oligo-mesotrophic, boreal lake (Lake Pääjärvi, Finland), under varying nitrate concentrations using ¹³ C-labelling. Furthermore, vertical profiles of the sediment and porewater geochemistry, and the microbial communities (16S rRNA gene and shotgun metagenomic sequencing) were analyzed. Despite geochemical data indicating that simultaneous consumption of nitrate and methane took place at the sediment layers chosen for incubations, AOM rate was not enhanced by nitrate amendments at either of the stations. AOM rate was much higher at the shallow Station 1 (0.9-6.8 nmol C cm ^-3 d ^-1 ) with high contents of labile phytoplankton-derived organic matter, than at the deeper stations, Station 2 (0-0.3 nmol C cm ^-3 d ^-1 ) and 3 (0-0.2 nmol C cm ^-3 d ^-1 ). Accordingly, a higher relative abundance of methanotrophic archaea ( Candidatus Methanoperedens) and bacteria ( Methylococcales ) were observed in the layers chosen for incubations at Station 1 than at the other stations. Besides nitrate, the geochemical profiles indicated that AOM was potentially coupled with iron or sulfate reduction at all stations. Furthermore, putative nitrite-reducing methanotrophs ( Ca . Methylomirabilis) were the most abundant methanotrophs above the incubation layer at Station 2 and 3, which suggests that nitrite reduction also plays a role in driving AOM in the study lake. We conclude that AOM is not uniquely coupled to nitrate reduction in sediments of nitrate-rich, oligo-mesotrophic, boreal lakes.

Hypoxia is common feature of eutrophic estuaries and semi-enclosed seas globally. One of the key factors driving hypoxia is nitrogen pollution. To gain more insight into the effects of hypoxia on estuarine nitrogen cycling, we measured potential nitrate reduction rates at different salinities and levels of hypoxia in a eutrophic temperate microtidal estuary, the Neuse River Estuary, North Carolina, USA. We also tested the effect of hydrogen sulfide and ferrous iron additions on the nitrate reduction pathways. Overall, DNRA dominated over denitrification in this periodically hypoxic estuary and there was no correlation between the potential nitrate reduction rates, salinity, or dissolved oxygen. However, when hypoxia lasted several months, denitrification capacity was almost completely lost, and nearly all nitrate added to the sediment was reduced via DNRA. Additions of hydrogen sulfide stimulated DNRA over denitrification. Additions of ferrous iron stimulated nitrate consumption; however, the end product of nitrate consumption was not clear. Interestingly, substantial nitrous oxide formation occurred in sediments that had experienced prolonged hypoxia and were amended with nitrate. Given expanding hypoxia predicted with climate change scenarios and the increasing nitrate loads to coastal systems, coastal sediments may lose their capability to mitigate nitrogen pollution due to DNRA dominating over denitrification during extended hypoxic periods.