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The epilimnion is the surface layer of a lake typically characterised as well mixed and is decoupled from the metalimnion due to a steep change in density. The concept of the epilimnion (and, more widely, the three-layered structure of a stratified lake) is fundamental in limnology, and calculating the depth of the epilimnion is essential to understanding many physical and ecological lake processes. Despite the ubiquity of the term, however, there is no objective or generic approach for defining the epilimnion, and a diverse number of approaches prevail in the literature. Given the increasing availability of water temperature and density profile data from lakes with a high spatio-temporal resolution, automated calculations, using such data, are particularly common, and they have vast potential for use with evolving long-term globally measured and modelled datasets. However, multi-site and multi-year studies, including those related to future climate impacts, require robust and automated algorithms for epilimnion depth estimation. In this study, we undertook a comprehensive comparison of commonly used epilimnion depth estimation methods, using a combined 17-year dataset, with over 4700 daily temperature profiles from two European lakes. Overall, we found a very large degree of variability in the estimated epilimnion depth across all methods and thresholds investigated and for both lakes. These differences, manifesting over high-frequency data, led to fundamentally different understandings of the epilimnion depth. In addition, estimations of the epilimnion depth were highly sensitive to small changes in the threshold value, complex thermal water column structures, and vertical data resolution. These results call into question the custom of arbitrary method selection and the potential problems this may cause for studies interested in estimating the ecological processes occurring within the epilimnion, multi-lake comparisons, or long-term time series analysis. We also identified important systematic differences between methods, which demonstrated how and why methods diverged. These results may provide rationale for future studies to select an appropriate epilimnion definition in light of their particular purpose and with awareness of the limitations of individual methods. While there is no prescribed rationale for selecting a particular method, the method which defined the epilimnion depth as the shallowest depth, where the density was 0.1 kg m -3 more than the surface density, may be particularly useful as a generic method. [ABSTRACT FROM AUTHOR]

Between May and July 2018, Ireland experienced an exceptional heat wave, which broke long-term temperature and drought records. These calm, stable conditions were abruptly interrupted by a second extreme weather event, Atlantic Storm Hector, in late June. Using high-frequency monitoring data, coupled with fortnightly biological sampling, we show that the storm directly affected the stratification pattern of Lough Feeagh, resulting in an intense mixing event. The lake restabilised quickly after the storm as the heatwave continued. During the storm there was a three-fold reduction in Schmidt stability, with a mixed layer deepening of 9.5 m coinciding with a two-fold reduction in chlorophyll a but a three-fold increase in total zooplankton biomass. Epilimnetic respiration increased and net ecosystem productivity decreased. The ratio of total nitrogen:total phosphorus from in-lake versus inflow rivers was decoupled, leading to a cascade effect on higher trophic levels. A step change in nitrogen:phosphorus imbalances suggested that the zooplankton community shifted from phosphorus to nitrogen nutrient constraints. Such characterisations of both lake thermal and ecological responses to extreme weather events are relatively rare but are crucial to our understanding of how lakes are changing as the impacts of global climate change accelerate. [ABSTRACT FROM AUTHOR]

Processing equipment and buildings at derelict mine sites are commonly coated in metal- and metalloid-rich residues that can significantly contribute to acid and metalliferous drainage, potentially polluting soils and watercourses. Here, we describe arsenic-rich residues and efflorescences on processing buildings at the derelict Ottery As–Sn mine in New South Wales, Australia and use the resulting data to determine the mineral hosts for arsenic and their distribution at the site. X-ray diffraction (XRD), portable X-ray fluorescence (XRF) and scanning electron microscopy (SEM) data are used to conduct mineralogical, geochemical and microstructural analysis of the efflorescences. Brickwork columns within As condenser buildings are coated primarily with gypsum (CaSO 4 ·2H 2 O) and contain approximately 1–5 wt% As, but more sheltered columns are associated with efflorescences rich in arsenolite and claudetite (polymorphs of As 2 O 3 ) and contain up to ∼70–80 wt% As. The efflorescences within the Ottery condensers commonly contain minor quartz (SiO 2 ), feldspars, and two uncharacterised phases, including a K-Al-As phase and a Ca-Na-K-Al-F-As phase that are likely similar to previously reported phases from an As processing site in Cornwall, UK. SEM imaging indicates that the weathering of mortar and bricks provides a source of cations for efflorescence formation, with grains of more resistant minerals (e.g., quartz) incorporated into the efflorescences. Arsenic does not appear to substitute significantly for S in gypsum but instead is generally hosted in (1) Al, Na, Ca and Fe-bearing arsenate minerals in weathered efflorescences and (2) in small grains of arsenolite in pore spaces within the brickwork, indicating that the bricks are a potentially long-lived source of As. The efflorescences on exposed columns at Ottery also regrow within 12 months after removal, releasing stored arsenic from the brickwork and causing a cyclical degradation of the buildings. Our results indicate that brickwork buildings at mine sites like Ottery initially act as significant sinks for As within arsenolite. Over time, this As can become mobilised by rainfall to form arsenate–sulfate efflorescences, which gradually become more sulfate-rich as the arsenate minerals are removed by weathering. Thus, remediation efforts at abandoned, As-bearing processing buildings, such as those at Ottery, should focus on preventing water contact with bricks and mortar within processing buildings as well as efflorescences. This research, combined with the remediation and research undertaken in similar areas such as the UNESCO Cornish Mining World Heritage Site in the UK, an area containing many derelict, arsenic-bearing processing buildings that have been successfully remediated and are now tourist attractions, indicates that a delicate balance needs to be found between remediation and resolving pollution issues and retaining the industrial heritage represented by these processing sites. [ABSTRACT FROM AUTHOR]

Violacein is a water-insoluble violet pigment produced by various Gram-negative bacteria. The compound and the bacteria that produce it have been gaining attention due to the antimicrobial and proposed antitumour properties of violacein and the possibility that strains producing it may have broad industrial uses. Bacteria that produce violacein have been isolated from diverse environments including fresh and ocean waters, glaciers, tropical soils, trees, fish and the skin of amphibians. We report here the isolation and characterization of six violacein-producing bacterial strains and three non-violacein-producing close relatives, each isolated from either an aquatic environment or moist food materials in northern California, USA. For each isolate, we characterized traditional phenotypes, generated and analysed draft genome sequences, and carried out multiple types of taxonomic, phylogenetic and phylogenomic analyses. Based on these analyses we assign putative identifications to the nine isolates, which include representatives of the genera Chromobacterium , Aquitalea , Iodobacter , Duganella , Massilia and Janthinobacterium . In addition, we discuss the utility of various metrics for taxonomic assignment in these groups including average nucleotide identity, whole genome phylogenetic analysis and extent of recent homologous recombination using the software program PopCOGenT.

Cold-tolerant bacteria are known to contaminate and cause defects in refrigerated foods. Defects in food products can be observed as changes in appearance, texture, and/or flavor that detract from the product's intended look, feel, or taste. Two distinct organisms were cultured from blue pigmented soymilk and tofu that had been left opened and expired in a home refrigerator. The blue coloration was reproduced when isolates were cultured in fresh, sterile soymilk. These strains also produced a variety of colony color morphologies when cultured on different media types. We report two draft genome sequences of the potential causative agents of blue discoloration of soy foods, Pseudomonas carnis strains UCD_MED3 and UCD_MED7 as well as the 16S rRNA gene sequences of co-occurring strains isolated from the defective soy samples but that did not cause blue discoloration when cultured in fresh soymilk; Serratia liquefaciens strains UCD_MED2 and UCD_MED5., Competing Interests: Competing Interests: The authors have declared that no competing interest exists., (© The author(s).)

In many regions across the globe, extreme weather events such as storms have increased in frequency, intensity, and duration due to climate change. Ecological theory predicts that such extreme events should have large impacts on ecosystem structure and function. High winds and precipitation associated with storms can affect lakes via short-term runoff events from watersheds and physical mixing of the water column. In addition, lakes connected to rivers and streams will also experience flushing due to high flow rates. Although we have a well-developed understanding of how wind and precipitation events can alter lake physical processes and some aspects of biogeochemical cycling, our mechanistic understanding of the emergent responses of phytoplankton communities is poor. Here we provide a comprehensive synthesis that identifies how storms interact with lake and watershed attributes and their antecedent conditions to generate changes in lake physical and chemical environments. Such changes can restructure phytoplankton communities and their dynamics, as well as result in altered ecological function (e.g., carbon, nutrient and energy cycling) in the short- and long-term. We summarize the current understanding of storm-induced phytoplankton dynamics, identify knowledge gaps with a systematic review of the literature, and suggest future research directions across a gradient of lake types and environmental conditions., (© 2020 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)

Three independent isolates of Gram-reaction-negative cocci collected from two New York State patients and a dog's mouth in California were subjected to a polyphasic analysis. The 16S rRNA gene sequence similarity among these isolates is 99.66 to 99.86 %. The closest species with a validly published name is Neisseria zoodegmatis (98.7 % 16S rRNA gene sequence similarity) with six additional species of the genus Neisseria with greater than 97 % similarity. Average nucleotide identity (ANI) and genome-to-genome distance calculator (GGDC 2.0) analysis on whole genome sequence data support the three novel isolates as being from a single species that is distinct from all other closely related species of the genus Neisseria. Phylogenetic analysis of 16S rRNA gene sequences and ribosomal multilocus sequence typing (rMLST) indicate the novel species belongs in the genus Neisseria. This assignment is further supported by the predominant cellular fatty acids composition of C16 : 0, summed feature 3 (C16 : 1ω7c/C15 : 0iso 2-OH), and C18 : 1ω7c, and phenotypic characters. The name Neisseria dumasiana sp. nov. is proposed, and the type strain is 93087 T (=DSM 104677 T =LMG 30012 T ).