Single-Use Plastics and COVID-19: Scientific Evidence and Environmental Regulations

Waste plastics are a serious and growing environmental problem. Less than 10% of plastics are recycled, with most discarded in landfills, incinerated, or simply abandoned.1 Single-use plastics constitute about half of plastic waste. While most plastics are used and initially disposed of on land, much eventually enters aquatic ecosystems.2 Wildlife mortalities result from encounters (e.g., ingestion and entanglement) with large debris, including plastic bags. Such bags are excluded from many recycling programs, as they can entangle machinery. Most plastics do not readily biodegrade in the environment. However, they can be embrittled by UV exposure and fragment into microplastics (mm) and nanoplastics

Enhanced Nitrous Oxide Production in Denitrifying Dechloromonas aromatica Strain RCB Under Salt or Alkaline Stress Conditions

Salinity and pH have direct and indirect impacts on the growth and metabolic activities of microorganisms. In this study, the effects of salt and alkaline stresses on the kinetic balance between nitrous oxide (N2O) production and consumption in the denitrification pathway of Dechloromonas aromatica strain RCB were examined. N2O accumulated transiently only in insignificant amounts at low salinity

Vertical Stratification of Sediment Microbial Communities Along Geochemical Gradients of a Subterranean Estuary Located at the Gloucester Beach of Virginia, United States

Subterranean estuaries (STEs) have been recognized as important ecosystems for the exchange of materials between the land and sea, but the microbial players of biogeochemical processes have not been well examined. In this study, we investigated the bacterial and archaeal communities within 10 cm depth intervals of a permeable sediment core (100 cm in length) collected from a STE located at Gloucester Point (GP-STE), VA, United States. High throughput sequencing of 16S rRNA genes and subsequent bioinformatics analyses were conducted to examine the composition, diversity, and potential functions of the sediment communities. The community composition varied significantly from the surface to a depth of 100 cm with up to 13,000 operational taxonomic units (OTUs) based on 97% sequence identities. More than 95% of the sequences consisted of bacterial OTUs, while the relative abundances of archaea, dominated by Crenarchaea, gradually increased with sediment core depth. Along the redox gradients of GP-STE, differential distribution of ammonia-and methane-oxidizing, denitrifying, and sulfate reducing bacteria was observed as well as methanogenic archaea based on predicted microbial functions. The aerobic-anaerobic transition zone (AATZ) had the highest diversity and abundance of microorganisms, matching with the predicted functional diversity. This indicates the AATZ as a hotspot of biogeochemical processes of STEs. The physical and geochemical gradients in different depths have attributed to vertical stratification of microbial community composition and function in the GP-STE

Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils

Microorganisms are capable of producing N-2 and N2O gases as the end products of denitrification. Copper-containing nitrite reductase (NirK), a key enzyme in the microbial N-cycle, has been found in bacteria, archaea and fungi. This study seeks to assess the diversity of nirK genes in the prokaryotic and fungal communities of agricultural soils in the United States. New primers targeting the nirK genes in fungi were developed, while nirK genes in archaea and bacteria were detected using previously published methods. The new primers were able to detect fungal nirK genes as well as bacterial nirK genes from a group that could not be observed with previously published primers. Based on the sequence analyses from three different primer sets, five clades of nirK genes were identified, which were associated with soil archaea, ammonium-oxidizing bacteria, denitrifying bacteria and fungi. The diversity of nirK genes in the two denitrifying bacteria clades was higher than the diversity found in other clades. Using a newly designed primer set, this study showed the detection of fungal nirK genes from environmental samples. The newly designed PCR primers in this study enhance the ability to detect the diversity of nirK-encoding microorganisms in soils

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

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 (N-2) as the end-products of denitrification. Grassland soils were pre-incubated with and without tetracycline for 1-week prior to measurements of N2O and N-2 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 N-2 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

Genetic and biogeochemical investigation of sedimentary nitrogen cycling communities responding to tidal and seasonal dynamics in Cape Fear River Estuary

Tidal and seasonal fluctuations in the oligohaline reaches of estuaries may alter geochemical features that influence structure and function of microbial communities involved in sedimentary nitrogen (N) cycling. In order to evaluate sediment community responses to short-term (tidal) and long-term (seasonal) changes in different tidal regimes, nitrogen cycling rates and genes were quantified in three sites that span a range of tidal influence in the upper portion of the Cape Fear River Estuary. Environmental parameters were monitored during low and high tides in winter and spring. N-15 tracer incubation experiments were conducted to measure nitrification, denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonia (DNRA). Abundances of functional genes including bacterial and archaeal ammonia monooxygenase (amoA), nitrite reductases (nirS and nrfA), nitrous oxide reductase (nosZ), and hydrazine oxidoreductase (hzo) were measured using quantitative PCR assays. Denitrification rates were highest among the measured N cycling processes while bacteria carrying nrfA genes were most abundant. A discernable pattern in the short-term variation of N cycling rates and gene abundance was not apparent under the different tidal regimes. Significant seasonal variation in nitrification, denitrification, and anammox rates as well as bacterial amoA, nirS and nosZ gene abundance was observed, largely explained by increases in substrate availability during winter, with sediment ammonium playing a central role. These results suggest that the coupling of nitrification to N removal pathways is primarily driven by organic carbon mineralization and independent of tidal or salinity changes. Finally, changes in denitrification and nitrification activities were strongly reflected by the abundance of the respective functional genes, supporting a linkage between the structure and function of microbial communities. (c) 2015 Elsevier Ltd. All rights reserved

Mesozooplankton Graze on Cyanobacteria in the Amazon River Plume and Western Tropical North Atlantic

Diazotrophic cyanobacteria, those capable of fixing di-nitrogen (N2), are considered one of the major sources of new nitrogen (N) in the oligotrophic tropical ocean, but direct incorporation of diazotrophic N into food webs has not been fully examined. In the Amazon River-influenced western tropical North Atlantic (WTNA), diatom diazotroph associations (DDAs) and the filamentous colonial diazotrophs Trichodesmium have seasonally high abundances. We sampled epipelagic mesozooplankton in the Amazon River plume and WTNA in May-June 2010 to investigate direct grazing by mesozooplankton on two DDA populations: Richelia associated with Rhizosolenia diatoms (het-1) and Hemiaulus diatoms (het-2), and on Trichodesmium using highly specific qPCR assays targeting nitrogenase genes (nifH). Both DDAs and Trichodesmium occurred in zooplankton gut contents, with higher detection of het-2 predominantly in calanoid copepods (2.33-16.76 nifH copies organism 1). Abundance of Trichodesmium was low (2.21-4.03 nifH copies organism 1), but they were consistently detected at high salinity stations (\u3e 35) in calanoid copepods. This suggests direct grazing on DDAs, Trichodesmium filaments and colonies, or consumption as part of sinking aggregates, is common. In parallel with the qPCR approach, a next generation sequencing analysis of 16S rRNA genes identified that cyanobacterial assemblage associated with zooplankton guts was dominated by the non-diazotrophic unicellular phylotypes Synechococcus (56%) and Prochlorococcus (26%). However, in two separate calanoid copepod samples, two unicellular diazotrophs Candidatus Atelocyanobacterium thalassa (UCYN-A) and Crocosphaera watsonii (UCYN-B) were present, respectively, as a small component of cyanobacterial assemblages (\u3c 2%). This study represents the first evidence of consumption of DDAs, Trichodesmium, and unicellular cyanobacteria by calanoid copepods in an area of the WTNA known for high carbon export. These diazotroph populations are quantitatively important in the global N budget, widespread and hence, the next step is to accurately quantify grazing. Nonetheless, these results highlight a direct pathway of diazotrophic N into the food web and have important implications for biogeochemical cycles, particularly oligotrophic regions where N-2 fixation is the main source of new nitrogen

Denitrification potential of the eastern oyster microbiome using a 16S rRNA gene based metabolic inference approach

The eastern oyster (Crassostrea virginica) is a foundation species providing significant ecosystem services. However, the roles of oyster microbiomes have not been integrated into any of the services, particularly nitrogen removal through denitrification. We investigated the composition and denitrification potential of oyster microbiomes with an approach that combined 16S rRNA gene analysis, metabolic inference, qPCR of the nitrous oxide reductase gene (nosZ), and N-2 flux measurements. Microbiomes of the oyster digestive gland, the oyster shell, and sediments adjacent to the oyster reef were examined based on next generation sequencing (NGS) of 16S rRNA gene amplicons. Denitrification potentials of the microbiomes were determined by metabolic inferences using a customized denitrification gene and genome database with the paprica (PAthway PRediction by phylogenetIC plAcement) bioinformatics pipeline. Denitrification genes examined included nitrite reductase (nirS and nirK) and nitrous oxide reductase (nosZ), which was further subdivided by genotype into clade I (nosZI) or clade II (nosZII). Continuous flow through experiments measuring N-2 fluxes were conducted with the oysters, shells, and sediments to compare denitrification activities. Paprica properly classified the composition of microbiomes, showing similar classification results from Silva, Greengenes and RDP databases. Microbiomes of the oyster digestive glands and shells were quite different from each other and from the sediments. The relative abundance of denitrifying bacteria inferred by paprica was higher in oysters and shells than in sediments suggesting that oysters act as hotspots for denitrification in the marine environment. Similarly, the inferred nosZI gene abundances were also higher in the oyster and shell microbiomes than in the sediment microbiome. Gene abundances for nosZI were verified with qPCR of nosZI genes, which showed a significant positive correlation (F-1,F-7 = 14.7, p = 6.0x10(-3), R-2 = 0.68). N-2 flux rates were significantly higher in the oyster (364.4 +/- 23.5 mu mol N-N-2 m(-2) h(-1)) and oyster shell (355.3 +/- 6.4 mu mol N-N-2 m(-2) h(-1)) compared to the sediment (270.5 +/- 20.1 mu mol N-N-2 m(-2) h(-1)). Thus, bacteria carrying nosZI genes were found to be an important denitrifier, facilitating nitrogen removal in oyster reefs. In addition, this is the first study to validate the use of 16S gene based metabolic inference as a method for determining microbiome function, such as denitrification, by comparing inference results with qPCR gene quantification and rate measurements

Microplastics affect sedimentary microbial communities and nitrogen cycling

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

Differential effects of bivalves on sediment nitrogen cycling in a shallow coastal bay

In coastal ecosystems, suspension-feeding bivalves can remove nitrogen though uptake and assimilation or enhanced denitrification. Bivalves may also retain nitrogen through increased mineralization and dissimilatory nitrate reduction to ammonium (DNRA). This study investigated the effects of oyster reefs and clam aquaculture on denitrification, DNRA, and nutrient fluxes (NOx, NH4 6 +, O2). Core incubations were conducted seasonally on sediments adjacent to restored oyster reefs (Crassostrea virginica), clam aquaculture beds (Mercenaria mercenaria) which contained live clams, and bare sediments from Smith Island Bay, Virginia, USA. Denitrification was significantly higher at oyster reef sediments and clam aquaculture site than bare sediment in the summer; however DNRA was not enhanced. The clam aquaculture site had the highest ammonium production due to clam excretion. While oyster reef and bare sediments exhibited seasonal differences in rate processes, there was no effect of season on denitrification, DNRA or ammonium flux at the clam aquaculture site. This suggests that farm management practices or bivalve metabolism and excretion may override seasonal differences. When water column nitrate concentration was elevated, denitrification increased in clam aquaculture site and oyster reef sediments but not in bare sediment; DNRA was only stimulated at the clam aquaculture site. This, along with a significant and positive relationship between denitrification and sediment organic matter, suggests that labile carbon limited nitrate reduction at the bare sediment site. Bivalve systems can serve as either net sinks or sources of nitrogen to coastal ecosystems, depending mainly on the type of bivalve, location and management practices