Isolation of a Dissimilatory Iodate-Reducing Aromatoleum sp. From a Freshwater Creek in the San Francisco Bay Area

Recent reports of dissimilatory iodate-reducing microorganisms (DIRM) have arisen from studies of bacteria in marine environments. These studies described the physiology and distribution of DIRM while also demonstrating their presence in iodine-rich marine environments. We posited that despite lower iodine concentrations, terrestrial and freshwater ecosystems should also harbor DIRM. We established numerous enrichments from coastal and freshwater environments that actively remove amended iodate. We describe the physiology and genome of a new DIRM isolate, Aromatoleum toluclasticum sp. TC-10, emerging from a freshwater creek microcosm. Like other DIRM, A. toluclasticum sp. TC-10 couples acetate oxidation to iodate reduction with a concomitant increase in the OD600. Our results indicate that A. toluclasticum sp. TC-10 performs dissimilatory iodate reduction (DIR) using the recently described iodate reductase (Idr). We provide further evidence of horizontal gene transfer of the idr genes by demonstrating the lack of Idr in the closely related (99.93% 16S rDNA sequence identity) A. toluclasticum sp. MF63 and describe the heterogeneity of the accessory proteins associated with the iodate reduction island (IRI). These observations provide additional evidence that DIR is a horizontally acquired metabolism with broad environmental distribution beyond exclusively marine environments.

Sustainable management of populations impacted by harvesting and climate change

The sustainable use of natural resources is critical for addressing the global challenges of today. Strategies for sustainable harvesting need to consider not only harvested species, but also other non-harvested species interacting with them in the same ecosystem. In addition, environmental variation needs to be considered, with climate change currently being one of the main sources of this variation. Understanding the consequences of complex interactions between different drivers and processes affecting dynamics of species and ecosystems across spatial scales requires large-scale integrative research projects. The Norwegian research initiative “Sustainable management of renewable resources in a changing environment: an integrated approach across ecosystems” (SUSTAIN) was launched to fill knowledge gaps related to the sustainable management of populations and ecosystems experiencing climate change. SUSTAIN investigated terrestrial, marine and freshwater ecosystems in boreal and Arctic regions, using both theoretical developments and empirical analyses of long-term data. This Climate Research Special contains both synthesis articles and original research exemplifying some of the approaches used in SUSTAIN. In this introduction we highlight 4 key topics addressed by SUSTAIN: (i) population structure, (ii) interactions between species, (iii) spatial processes, and (iv) adaptive management. These topics are fundamental to the understanding of harvested species from an ecosystem perspective, and to ecosystem-based management approaches, which we are striving to work towards.

The role of methanotrophy in the microbial carbon metabolism of temperate lakes

Previous stable isotope and biomarker evidence has indicated that methanotrophy is an important pathway in the microbial loop of freshwater ecosystems, despite the low cell abundance of methane-oxidizing bacteria (MOB) and the low methane concentrations relative to the more abundant dissolved organic carbon (DOC). However, quantitative estimations of the relative contribution of methanotrophy to the microbial carbon metabolism of lakes are scarce, and the mechanism allowing methanotrophy to be of comparable importance to DOC-consuming heterotrophy remained elusive. Using incubation experiments, microscopy, and multiple water column profiles in six temperate lakes, we show that MOB play a much larger role than their abundances alone suggest because of their larger cell size and higher specific activity. MOB activity is tightly constrained by the local methane:oxygen ratio, with DOC-rich lakes with large hypolimnetic volume fraction showing a higher carbon consumption through methanotrophy than heterotrophy at the whole water column level. Our findings suggest that methanotrophy could be a critical microbial carbon consumption pathway in many temperate lakes, challenging the prevailing view of a DOC-centric microbial metabolism in these ecosystems.

Microbial diversity in intensively farmed lake sediment contaminated by heavy metals and identification of microbial taxa bioindicators of environmental quality

The cumulative effects of anthropogenic stress on freshwater ecosystems are becoming increasingly evident and worrisome. In lake sediments contaminated by heavy metals, the composition and structure of microbial communities can change and affect nutrient transformation and biogeochemical cycling of sediments. In this study, bacterial and archaeal communities of lake sediments under fish pressure contaminated with heavy metals were investigated by the Illumina MiSeq platform. Despite the similar content of most of the heavy metals in the lagoon sediments, we found that their microbial communities were different in diversity and composition. This difference would be determined by the resilience or tolerance of the microbial communities to the heavy metal enrichment gradient. Thirty-two different phyla and 66 different microbial classes were identified in sediment from the three lagoons studied. The highest percentages of contribution in the differentiation of microbial communities were presented by the classes Alphaproteobacteria (19.08%), Cyanophyceae (14.96%), Betaproteobacteria (9.01%) y Actinobacteria (7.55%). The bacteria that predominated in sediments with high levels of Cd and As were Deltaproteobacteria, Actinobacteria, Coriobacteriia, Nitrososphaeria and Acidobacteria (Pomacocha), Alphaproteobacteria, Chitinophagia, Nitrospira and Clostridia (Tipicocha) and Betaproteobacteria (Tranca Grande). Finally, the results allow us to expand the current knowledge of microbial diversity in lake sediments contaminated with heavy metals and to identify bioindicators taxa of environmental quality that can be used in the monitoring and control of heavy metal contamination.

A First Glimpse on Cold-Adapted PCB-Oxidizing Bacteria in Edmonson Point Lakes (Northern Victoria Land, Antarctica)

Antarctic freshwater ecosystems are especially vulnerable to human impacts. Polychlorobiphenyls (PCBs) are persistent organic pollutants that have a long lifetime in the environment. Despite their use having either been phased out or restricted, they are still found in nature, also in remote areas. Once in the environment, the fate of PCBs is strictly linked to bacteria which represent the first step in the transfer of toxic compounds to higher trophic levels. Data on PCB-oxidizing bacteria from polar areas are still scarce and fragmented. In this study, the occurrence of PCB-oxidizing cold-adapted bacteria was evaluated in water and sediment of four coastal lakes at Edmonson Point (Northern Victoria Land, Antarctica). After enrichment with biphenyl, 192 isolates were obtained with 57 of them that were able to grow in the presence of the PCB mixture Aroclor 1242, as the sole carbon source. The catabolic gene bphA, as a proxy for PCB degradation potential, was harbored by 37 isolates (out of 57), mainly affiliated to the genera Salinibacterium, Arthrobacter (among Actinobacteria) and Pusillimonas (among Betaproteobacteria). Obtained results enlarge our current knowledge on cold-adapted PCB-oxidizing bacteria and pose the basis for their potential application as a valuable eco-friendly tool for the recovery of PCB-contaminated cold sites.

Are nitrogen and carbon cycle processes impacted by common stream antibiotics? A comparative assessment of single vs. mixture exposures

A variety of antibiotics are ubiquitous in all freshwater ecosystems that receive wastewater. A wide variety of antibiotics have been developed to kill problematic bacteria and fungi through targeted application, and their use has contributed significantly to public health and livestock management. Unfortunately, a substantial fraction of the antibiotics applied to humans, pets and livestock end up in wastewater, and ultimately many of these chemicals enter freshwater ecosystems. The effect of adding chemicals that are intentionally designed to kill microbes, on freshwater microbial communities remains poorly understood. There are reasons to be concerned, as microbes play an essential role in nutrient uptake, carbon fixation and denitrification in freshwater ecosystems. Chemicals that reduce or alter freshwater microbial communities might reduce their capacity to degrade the excess nutrients and organic matter that characterize wastewater. We performed a laboratory experiment in which we exposed microbial community from unexposed stream sediments to three commonly detected antibiotics found in urban wastewater and urban streams (sulfamethoxazole, danofloxacin, and erythromycin). We assessed how the form and concentration of inorganic nitrogen, microbial carbon, and nitrogen cycling processes changed in response to environmentally relevant doses (10 μg/L) of each of these antibiotics individually and in combination. We expected to find that all antibiotics suppressed rates of microbial mineralization and nitrogen transformations and we anticipated that this suppression of microbial activity would be greatest in the combined treatment. Contrary to our expectations we measured few significant changes in microbially mediated functions in response to our experimental antibiotic dosing. We found no difference in functional gene abundance of key nitrogen cycling genes nosZ, mcrA, nirK, and amoA genes, and we measured no treatment effects on NO3- uptake or N2O, N2, CH4, CO2 production over the course of our seven-day experiment. In the mixture treatment, we measured significant increases in NH4+ concentrations over the first 24 hours of the experiment, which were indistinguishable from controls within six hours. Our results suggest remarkable community resistance to pressure antibiotic exposure poses on naïve stream sediments.

Cyanopeptides Restriction and Degradation Co-mediate Microbiota Assembly During a Freshwater Cyanobacterial Harmful Algal Bloom (CyanoHAB)

Cyanobacterial harmful algal blooms (CyanoHABs) are globally intensifying and exacerbated by climate change and eutrophication. However, microbiota assembly mechanisms underlying CyanoHABs remain scenario specific and elusive. Especially, cyanopeptides, as a group of bioactive secondary metabolites of cyanobacteria, could affect microbiota assembly and ecosystem function. Here, the trajectory of cyanopeptides were followed and linked to microbiota during Microcystis-dominated CyanoHABs in lake Taihu, China. The most abundant cyanopeptide classes detected included microginin, spumigin, microcystin, nodularin and cyanopeptolin with total MC-LR-equivalent concentrations between 0.23 and 2051.54 ppb, of which cyanotoxins beyond microcystins (e.g., cyanostatin B and nodularin_R etc.) far exceeded reported organismal IC50 and negatively correlated with microbiota diversity, exerting potential collective eco-toxicities stronger than microcystins alone. The microbial communities were differentiated by size fraction and sampling date throughout CyanoHABs, and surprisingly, their variances were better explained by cyanopeptides (19-38%) than nutrients (0-16%). Cyanopeptides restriction (e.g., inhibition) and degradation are first quantitatively verified as the deterministic drivers governing community assembly, with stochastic processes being mediated by interplay between cyanopeptide dynamics and lake microbiota. This study presents an emerging paradigm in which cyanopeptides restriction and degradation co-mediate lake water microbiota assembly, unveiling new insights about the ecotoxicological significance of CyanoHABs to freshwater ecosystems.

The «Empty Forest Syndrome» and the Herpetofaunal Communities in Laos (South-Eastern Asia)

Nowadays, Laos remains one of the scientifically least known countries of Asia in terms of herpetological knowledge. Here, we evaluate composition of species in freshwater ecosystems (main river courses) and terrestrial ecosystems (forests) in two distinct regions using Visual Encounter Surveys along designed transects, examination of fishers’ catches and standardized interviews. In Northern Laos, we recorded only 18 reptile individuals (2 turtle and 1 snake species). Interview surveys demonstrated that in Nam Xam River, fishers are more likely to hunt turtles and we identified one potential site where the world’s rarest turtle, Rafetus swinhoei, could be still present in the wild. In Nam Et Phou Louey National Park, we found 19 reptile species (8 lizard, 10 snake, 1 turtle species) in the different study sites, demonstrating a low species density in all different surveyed habitats. In Central/Southern Laos, we observed 30 species of reptiles (14 snake, 16 lizard, 35 amphibian species). Our study offers preliminary insights into the composition of amphibians and reptiles in Laos. The great majority of the species were non-threatened or not evaluated, and a few were threatened, suggesting that more research is needed to proper understand the conservation status of Laos’ herpetofauna. We highlighted, indirectly by interviews with local fishers, the possible presence of the turtle Rafetus swinhoei, thus providing a new hope for avoiding the extinction of this species. Finally, we observed a relatively low number of species in each habitat type, which is remarkably lower than in tropical forests of other continents or of nearby south-east Asian countries, indicating that the herpetofauna communities in Laos are depleted, reflecting an ‘empty forest syndrome’.

The Occurrence of Intersex in Different Populations of the Marine Amphipod Echinogammarus marinus in North-West Brittany – A Longterm-Study

In the past two decades, an increasing body of studies has been published on the intersex phenomenon in separate-sexed crustaceans from marine and freshwater ecosystems. Various causes are being considered that could have an influence on the occurrence of intersex. Besides genetic factors, environmental conditions such as photoperiodicity, temperature, salinity and parasitism, but also environmental pollution with endocrine disrupting chemicals (EDCs) are discussed. As part of a long-term monitoring (2012 – 2020) in north-west Brittany, we recorded the occurrence of intersex in the marine amphipod Echinogammarus marinus. We quantified the intersex incidence at marine and estuarine sites and analyzed the incidence in relation to the endocrine potential of the sediments. Intersex occurred with mean frequencies between 0.87% and 12%. It was striking that the incidence of intersex increased with increasing distance from the sea. Since the highest incidence was observed at the range boundary of this stenohaline species, we assume that intersex is triggered by endocrine potential and increasing stress due to increasing freshwater content − and thus an interplay of different environmental factors.