High frequency environmental DNA metabarcoding provides rapid and effective monitoring of fish community dynamics

Long‐term monitoring is critical to measure the response of biodiversity patterns and processes to human‐mediated environmental pressures. This is particularly pertinent in freshwaters, where recent estimates indicated a third of all fish species are threatened with extinction, making ongoing biomonitoring essential for conservation management. High frequency annual monitoring is critical for identifying temporal changes in fish community composition; however, traditional survey methods are typically less practical over such timeframes. While environmental (e)DNA measurement represents a potentially powerful tool for monitoring temporal community dynamics, studies are lacking. To address this deficit, we generated a high frequency time‐series dataset of entire fish communities using eDNA metabarcoding, to directly assess the repeatability and sensitivity of this method for detecting annual population trends. We targeted two differing environments (freshwater vs. intertidal) within the Thames catchment, UK, where detailed historical records from traditional monitoring were available for comparison. To test how robust eDNA data is for inferring the known community, we applied a hierarchical, nested design encompassing short and longer‐term variation in eDNA data. Our analyses showed that irrespective of environment, eDNA metabarcoding represented known seasonal shifts in fish communities, where increased relative read abundance of eDNA coincided with known migratory and spawning events, including those of the critically endangered native species Anguilla anguilla (European eel). eDNA species detections across a single year included over 75% of species recorded in a ca. 30‐year historical dataset, highlighting the power of eDNA for species detection. Our findings provide greater insight into the utility of eDNA metabarcoding for recovering temporal trends in fish communities from dynamic freshwater systems and insight into the potential best sampling strategy for future eDNA surveys

Dealing with synthetics: time to reframe the narrative.

Key Points: • Despite adjustments over its lifetime, the contemporary international drug control regime has had an historical emphasis in on ‘narcotic’ drugs, such as opium, heroin and cocaine, rather than on a range of synthetic substances. • Associated policy inertia has resulted in disproportionate attention on counter-narcotic policies and operations in the Global South and in many ways inadequate responses to the synthetic market, including production that is frequently located in the Global North. • Possible explanations for this focus on plant-based drugs are manifold and complex. They include the fact that the control regime began with concerns over opium-smoking in the ‘orient’, a concentration of drug crops in the Global South, the energies of colonialism (which have been intimately tied up with ‘drug wars’), broader geo-political imperatives and the focus of policy metrics on drug crops. • The market for synthetic drugs has grown exponentially in recent years, becoming the second-most illicit drugs consumed after cannabis. In 2014, the UN estimated that there were 35.7 million users of amphetamine type stimulants (including prescription stimulants), and 19.4 million users of ecstasy. These synthetic drugs outstripped the estimated totals of opioids and cocaine combined. • Alongside this consumption is that of New Psychoactive Substances that fall outside the control regime and its schedules, which the regime is now attempting to integrate into national and international controls. • While there was some awareness of the advent of new synthetic drugs in the aftermath of the Second World War and since the 1960s, it is only over recent years, and especially in the wake of the 2016 UNGASS in New York, that a truly serious understanding of the challenges posed by proliferating synthetic drugs has begun to emerge from the international drug control regime. • This is timely since, considering its policy history and contemporary dynamics, it is now time to reframe the narrative surrounding the way the international community deals with synthetic drugs

Rates and Pathways of N2 Production in a Persistently Anoxic Fjord: Saanich Inlet, British Columbia

Marine oxygen minimum zones (OMZs) support 30–50% of global fixed-nitrogen (N) loss but comprise only 7% of total ocean volume. This N-loss is driven by canonical denitrification and anaerobic ammonium oxidation (anammox), and the distribution and activity of these two processes vary greatly in space and time. Factors that regulate N-loss processes are complex, including organic matter availability, oxygen concentrations, and NO2− and NH4+ concentrations. While both denitrification and anammox produce N2, the overall geochemical outcome of these processes are different, as incomplete denitrification, for example, produces N2O, which is a potent greenhouse gas. Information on rates of anammox and denitrification and more detailed ecophysiological knowledge of the microorganisms catalyzing these processes are needed to develop more robust models of N-loss in OMZs. To this end, we conducted monthly incubations with 15N-labeled N during under anoxic conditions and during a deep water renewal cycle in Saanich Inlet, British Columbia, a persistently anoxic fjord. Both denitrification and anammox operated throughout the low oxygen water column with depth integrated rates of anammox and denitrification ranging from 0.15 ± 0.03 to 3.4 ± 0.3 and 0.02 ± 0.006 to 14 ± 2 mmol N2 m−2 d−1, respectively. Most N2 production in Saanich Inlet was driven by denitrification, with high rates developing in response to enhanced substrate supply from deep water renewal. Dynamics in rates of denitrification were linked to shifts in microbial community composition. Notably, periods of intense denitrification were accompanied by blooms in an Arcobacter population against a background community dominated by SUP05 and Marinimicrobia. Rates of N2 production through denitrification and anammox, and their dynamics, were then explored through flux-balance modeling with higher rates of denitrification linked to the physiology of substrate uptake. Overall, both denitrification and anammox operated throughout the year, contributing to an annual N-loss of 2 × 10−3 Tg N2 yr−1, 37% of which we attribute to anammox and 63% to complete denitrification. Extrapolating these rates from Saanich Inlet to all similar coastal inlets in BC (2478 km2), we estimate that these inlets contribute 0.1% to global pelagic N-loss

The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity

Certain members of the Actinobacteria and Proteobacteria are known to degrade polyethylene terephthalate (PET). Here, we describe the first functional PET-active enzymes from the Bacteroidetes phylum. Using a PETase-specific Hidden-Markov-Model- (HMM-) based search algorithm, we identified several PETase candidates from Flavobacteriaceae and Porphyromonadaceae. Among them, two promiscuous and cold-active esterases derived from Aequorivita sp. (PET27) and Kaistella jeonii (PET30) showed depolymerizing activity on polycaprolactone (PCL), amorphous PET foil and on the polyester polyurethane Impranil® DLN. PET27 is a 37.8 kDa enzyme that released an average of 174.4 nmol terephthalic acid (TPA) after 120 h at 30°C from a 7 mg PET foil platelet in a 200 μl reaction volume, 38-times more than PET30 (37.4 kDa) released under the same conditions. The crystal structure of PET30 without its C-terminal Por-domain (PET30ΔPorC) was solved at 2.1 Å and displays high structural similarity to the IsPETase. PET30 shows a Phe-Met-Tyr substrate binding motif, which seems to be a unique feature, as IsPETase, LCC and PET2 all contain Tyr-Met-Trp binding residues, while PET27 possesses a Phe-Met-Trp motif that is identical to Cut190. Microscopic analyses showed that K. jeonii cells are indeed able to bind on and colonize PET surfaces after a few days of incubation. Homologs of PET27 and PET30 were detected in metagenomes, predominantly aquatic habitats, encompassing a wide range of different global climate zones and suggesting a hitherto unknown influence of this bacterial phylum on man-made polymer degradation

The higher-level phylogeny of Archosauria (Tetrapoda:Diapsida)

Crown group Archosauria, which includes birds, dinosaurs, crocodylomorphs, and several extinct Mesozoic groups, is a primary division of the vertebrate tree of life. However, the higher-level phylogenetic relationships within Archosauria are poorly resolved and controversial, despite years of study. The phylogeny of crocodile-line archosaurs (Crurotarsi) is particularly contentious, and has been plagued by problematic taxon and character sampling. Recent discoveries and renewed focus on archosaur anatomy enable the compilation of a new dataset, which assimilates and standardizes character data pertinent to higher-level archosaur phylogeny, and is scored across the largest group of taxa yet analysed. This dataset includes 47 new characters (25% of total) and eight taxa that have yet to be included in an analysis, and total taxonomic sampling is more than twice that of any previous study. This analysis produces a well-resolved phylogeny, which recovers mostly traditional relationships within Avemetatarsalia, places Phytosauria as a basal crurotarsan clade, finds a close relationship between Aetosauria and Crocodylomorpha, and recovers a monophyletic Rauisuchia comprised of two major subclades. Support values are low, suggesting rampant homoplasy and missing data within Archosauria, but the phylogeny is highly congruent with stratigraphy. Comparison with alternative analyses identifies numerous scoring differences, but indicates that character sampling is the main source of incongruence. The phylogeny implies major missing lineages in the Early Triassic and may support a Carnian-Norian extinction event.Marshall Scholarship for study in the United KingdomJurassic FoundationUniversity of BristolPaleontological Societ

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe

A communal catalogue reveals Earth’s multiscale microbial diversity

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity

The impact of immediate breast reconstruction on the time to delivery of adjuvant therapy: the iBRA-2 study

Background: Immediate breast reconstruction (IBR) is routinely offered to improve quality-of-life for women requiring mastectomy, but there are concerns that more complex surgery may delay adjuvant oncological treatments and compromise long-term outcomes. High-quality evidence is lacking. The iBRA-2 study aimed to investigate the impact of IBR on time to adjuvant therapy. Methods: Consecutive women undergoing mastectomy ± IBR for breast cancer July–December, 2016 were included. Patient demographics, operative, oncological and complication data were collected. Time from last definitive cancer surgery to first adjuvant treatment for patients undergoing mastectomy ± IBR were compared and risk factors associated with delays explored. Results: A total of 2540 patients were recruited from 76 centres; 1008 (39.7%) underwent IBR (implant-only [n = 675, 26.6%]; pedicled flaps [n = 105,4.1%] and free-flaps [n = 228, 8.9%]). Complications requiring re-admission or re-operation were significantly more common in patients undergoing IBR than those receiving mastectomy. Adjuvant chemotherapy or radiotherapy was required by 1235 (48.6%) patients. No clinically significant differences were seen in time to adjuvant therapy between patient groups but major complications irrespective of surgery received were significantly associated with treatment delays. Conclusions: IBR does not result in clinically significant delays to adjuvant therapy, but post-operative complications are associated with treatment delays. Strategies to minimise complications, including careful patient selection, are required to improve outcomes for patients

Standardized Assessment of Biodiversity Trends in Tropical Forest Protected Areas: The End Is Not in Sight

Extinction rates in the Anthropocene are three orders of magnitude higher than background and disproportionately occur in the tropics, home of half the world’s species. Despite global efforts to combat tropical species extinctions, lack of high-quality, objective information on tropical biodiversity has hampered quantitative evaluation of conservation strategies. In particular, the scarcity of population-level monitoring in tropical forests has stymied assessment of biodiversity outcomes, such as the status and trends of animal populations in protected areas. Here, we evaluate occupancy trends for 511 populations of terrestrial mammals and birds, representing 244 species from 15 tropical forest protected areas on three continents. For the first time to our knowledge, we use annual surveys from tropical forests worldwide that employ a standardized camera trapping protocol, and we compute data analytics that correct for imperfect detection. We found that occupancy declined in 22%, increased in 17%, and exhibited no change in 22% of populations during the last 3–8 years, while 39% of populations were detected too infrequently to assess occupancy changes. Despite extensive variability in occupancy trends, these 15 tropical protected areas have not exhibited systematic declines in biodiversity (i.e., occupancy, richness, or evenness) at the community level. Our results differ from reports of widespread biodiversity declines based on aggregated secondary data and expert opinion and suggest less extreme deterioration in tropical forest protected areas. We simultaneously fill an important conservation data gap and demonstrate the value of large-scale monitoring infrastructure and powerful analytics, which can be scaled to incorporate additional sites, ecosystems, and monitoring methods. In an era of catastrophic biodiversity loss, robust indicators produced from standardized monitoring infrastructure are critical to accurately assess population outcomes and identify conservation strategies that can avert biodiversity collapse. © 2016 Beaudrot et al