Microplastics are ubiquitous in estuarine, coastal, and deep sea sediments. The impacts of microplastics on sedimentary microbial ecosystems and biogeochemical carbon and nitrogen cycles, however, have not been well reported. To evaluate if microplastics influence the composition and function of sedimentary microbial communities, we conducted a microcosm experiment using salt marsh sediment amended with polyethylene (PE), polyvinyl chloride (PVC), polyurethane foam (PUF) or polylactic acid (PLA) microplastics. We report that the presence of microplastics alters sediment microbial community composition and nitrogen cycling processes. Compared to control sediments without microplastic, PUF- and PLA-amended sediments promote nitrification and denitrification, while PVC amendment inhibits both processes. These results indicate that nitrogen cycling processes in sediments can be significantly affected by different microplastics, which may serve as organic carbon substrates for microbial communities. Considering this evidence and increasing microplastic pollution, the impact of plastics on global ecosystems and biogeochemical cycling merits critical investigation. Plastic pollution has infiltrated every ecosystem, but few studies have quantified the biogeochemical or ecological effects of plastic. Here the authors show that microplastics in ocean sediment can significantly alter microbial community structure and nitrogen cycling.

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Microplastics affect sedimentary microbial communities and nitrogen cycling.

The recent literature describing polycyclic aromatic hydrocarbons (PAHs) in air, water, soil and sediment, waste sludge, biomonitoring, toxicity, are reviewed. Aspects of sampling, sample preparati...

Polycyclic aromatic hydrocarbons. A review

Sequencing of 16S rRNA genes has become a powerful technique to study microbial communities and their responses towards changing environmental conditions in various ecosystems. Several tools have been developed for the prediction of functional profiles from 16S rRNA gene sequencing data, because numerous questions in ecosystem ecology require knowledge of community functions in addition to taxonomic composition. However, the accuracy of these tools relies on functional information derived from genomes available in public databases, which are often not representative of the microorganisms present in the studied ecosystem. In addition, there is also a lack of tools to predict functional gene redundancy in microbial communities. To address these challenges, we developed Tax4Fun2, an R package for the prediction of functional profiles and functional gene redundancies of prokaryotic communities from 16S rRNA gene sequences. We demonstrate that functional profiles predicted by Tax4Fun2 are highly correlated to functional profiles derived from metagenomes of the same samples. We further show that Tax4Fun2 has higher accuracies than PICRUSt and Tax4Fun. By incorporating user-defined, habitat-specific genomic information, the accuracy and robustness of predicted functional profiles is substantially enhanced. In addition, functional gene redundancies predicted with Tax4Fun2 are highly correlated to functional gene redundancies determined for simulated microbial communities. Tax4Fun2 provides researchers with a unique tool to predict and investigate functional profiles of prokaryotic communities based on 16S rRNA gene sequencing data. It is easy-to-use, platform-independent and highly memory-efficient, thus enabling researchers without extensive bioinformatics knowledge or access to high-performance clusters to predict functional profiles. Another unique feature of Tax4Fun2 is that it allows researchers to calculate the redundancy of specific functions, which is a potentially important measure of how resilient a community will be to environmental perturbation. Tax4Fun2 is implemented in R and freely available at https://github.com/bwemheu/Tax4Fun2.

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Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences.

Metal in the environment arises from both natural sources and human activities. Toxic metals in air, soil, and water have become a global problem. They are potential hazards to aquatic, animal, and human life because of their toxicity, bioaccumulative, and non-biodegradable nature. The major impacts of metal pollutants can be stated as ecosystem contamination and health problems of exposed human populations. Those problems have been a cause of increasing public concern throughout the world. Some trace metals are used by living organisms to stabilize protein structures, facilitate electron transfer reactions, and catalyze enzymatic reactions. But even metals that are biologically essential can be harmful to living organisms at high levels of exposure. An increasing concentration of heavy metals in the environment can modify mineral and enzyme functions of human beings. During the last two decades, the interest in using bioindicators as monitoring tools to assess environmental pollution with toxic metals has increased. Bioindicators are flora and fauna members, which are collected and analyzed to measure the levels of metal contaminants. Bioindicators therefore identify health hazards. Various living organisms, such as microbes, fungi, plants, animals, and humans, are used to monitor toxic metals from air, water, sediment, soil, and food chain. Here, we review recent bioindicators, toxicity assessment, and ecological effects.

Biota as toxic metal indicators

Cephalopods have been utilised in neuroscience research for more than 100 years particularly because of their phenotypic plasticity, complex and centralised nervous system, tractability for studies of learning and cellular mechanisms of memory (e.g. long-term potentiation) and anatomical features facilitating physiological studies (e.g. squid giant axon and synapse). On 1 January 2013, research using any of the about 700 extant species of “live cephalopods” became regulated within the European Union by Directive 2010/63/EU on the “Protection of Animals used for Scientific Purposes”, giving cephalopods the same EU legal protection as previously afforded only to vertebrates. The Directive has a number of implications, particularly for neuroscience research. These include: (1) projects will need justification, authorisation from local competent authorities, and be subject to review including a harm-benefit assessment and adherence to the 3Rs principles (Replacement, Refinement and Reduction). (2) To support project evaluation and compliance with the new EU law, guidelines specific to cephalopods will need to be developed, covering capture, transport, handling, housing, care, maintenance, health monitoring, humane anaesthesia, analgesia and euthanasia. (3) Objective criteria need to be developed to identify signs of pain, suffering, distress and lasting harm particularly in the context of their induction by an experimental procedure. Despite diversity of views existing on some of these topics, this paper reviews the above topics and describes the approaches being taken by the cephalopod research community (represented by the authorship) to produce “guidelines” and the potential contribution of neuroscience research to cephalopod welfare.

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Cephalopods in neuroscience: regulations, research and the 3Rs

Metal accumulation and oxidative stress biomarkers in octopus (Octopus vulgaris) from Northwest Atlantic.

Antibiotics in soils may affect the structure and function of microbial communities In this study, we investigated the acute effects of tetracycline on soil microbial community composition and production of nitrous oxide (N2O) and dinitrogen (N2) as the end-products of denitrification Grassland soils were pre-incubated with and without tetracycline for 1-week prior to measurements of N2O and N2 production in soil slurries along with the analysis of prokaryotic and fungal communities by quantitative polymerase chain reaction (qPCR) and next-generation sequencing Abundance and taxonomic composition of bacteria carrying two genotypes of N2O reductase genes (nosZ-I and nosZ-II) were evaluated through qPCR and metabolic inference Soil samples treated with tetracycline generated 12 times more N2O, but N2 production was reduced by 84% compared to the control In parallel with greater N2O production, we observed an increase in the fungi:bacteria ratio and a significant decrease in the abundance of nosZ-II carrying bacteria; nosZ-I abundance was not affected NosZ-II-carrying Bacillus spp (Firmicutes) and Anaeromyxobacter spp (Deltaproteobacteria) were particularly susceptible to tetracycline and may serve as a crucial N2O sink in grassland soils Our study indicates that the introduction of antibiotics to agroecosystems may promote higher N2O production due to the inhibitory effects on nosZ-II-carrying communities

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Antibiotic Effects on Microbial Communities Responsible for Denitrification and N2O Production in Grassland Soils

SARS-CoV-2 RNA detected in urban wastewater from Porto, Portugal: Method optimization and continuous 25-week monitoring

Seasonal patterns of polycyclic aromatic hydrocarbons in digestive gland and arm of octopus (Octopus vulgaris) from the Northwest Atlantic.

The intensification of the poultry industry in the last decades has led to a sharp increase in the number of animal processing plants discharging wastewater to water bodies. These discharges may ha...

Miguel Semedo

Papers

Metal accumulation and oxidative stress biomarkers in octopus (Octopus vulgaris) from Northwest Atlantic.

Antibiotic Effects on Microbial Communities Responsible for Denitrification and N2O Production in Grassland Soils

SARS-CoV-2 RNA detected in urban wastewater from Porto, Portugal: Method optimization and continuous 25-week monitoring

Seasonal patterns of polycyclic aromatic hydrocarbons in digestive gland and arm of octopus (Octopus vulgaris) from the Northwest Atlantic.

From Genes to Nitrogen Removal: Determining the Impacts of Poultry Industry Wastewater on Tidal Creek Denitrification.