Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation.

Using new satellite observations and atmospheric inverse modeling, we report methane emissions from the Permian Basin, which is among the world’s most prolific oil-producing regions and accounts for >30% of total U.S. oil production. Based on satellite measurements from May 2018 to March 2019, Permian methane emissions from oil and natural gas production are estimated to be 2.7 ± 0.5 Tg a−1, representing the largest methane flux ever reported from a U.S. oil/gas-producing region and are more than two times higher than bottom-up inventory-based estimates. This magnitude of emissions is 3.7% of the gross gas extracted in the Permian, i.e., ~60% higher than the national average leakage rate. The high methane leakage rate is likely contributed by extensive venting and flaring, resulting from insufficient infrastructure to process and transport natural gas. This work demonstrates a high-resolution satellite data–based atmospheric inversion framework, providing a robust top-down analytical tool for quantifying and evaluating subregional methane emissions.

Dimethylsulfoniopropionate (DMSP) and its catabolite dimethyl sulfide (DMS) are key marine nutrients 1,2 , with roles in global sulfur cycling 2 , atmospheric chemistry 3 , signalling 4,5 and, potentially, climate regulation 6,7. DMSP production was previously thought to be an oxic and photic process, mainly confined to the surface oceans. 2 However, here we show that DMSP concentrations and DMSP/DMS synthesis rates were higher in surface marine sediment from e.g., saltmarsh ponds, estuaries and the deep ocean than in the overlying seawater. A quarter of bacterial strains isolated from saltmarsh sediment produced DMSP (up to 73 mM), and previously unknown DMSPproducers were identified. Most DMSP-producing isolates contained dsyB 8 , but some alphaproteobacteria, gammaproteobacteria and actinobacteria utilised a methionine methylation pathway independent of DsyB, previously only associated with higher plants. These bacteria contained a methionine methyltransferase 'mmtN' gene-a marker for bacterial DMSP synthesis via this pathway. DMSP-producing bacteria and their dsyB and/or mmtN transcripts were present in all tested seawater samples and Tara Oceans bacterioplankton datasets, but were far more abundant in marine surface sediment. Approximately 10 8 bacteria per gram of surface marine sediment are predicted to produce DMSP, and their contribution to this process should be included in future models of global DMSP production. We propose that coastal and marine sediments, which cover a large part of the Earth's surface, are environments with high DMSP and DMS productivity, and that bacteria are important producers within them. Approximately eight billion tonnes of DMSP is produced by phytoplankton in the Earth's surface oceans annually 9. However, surface sediment from saltmarsh ponds, an estuary and the deep ocean (with high pressures and no light) contained DMSP levels (5-128 nmol DMSP g-1) that were up to ~three orders of magnitude higher than the overlying seawater (0.01-0.70 nmol DMSP ml-1) (Fig. 1a-b, Supplementary Tables 1a and 2), a phenomenon also observed in 10,11. DMSP concentration decreased with depth, being much lower in anoxic sediment, but even in deeper sediments the concentration was approximately an order of magnitude higher than in the overlying seawater (Supplementary Table 1a). This study focused on DMSP synthesis in coastal surface sediments, where DMSP concentrations were highest. The

Since its first confirmed case at the end of 2019, COVID-19 has become a global pandemic in three months with more than 1.4 million confirmed cases worldwide, as of early April 2020. Quantifying the changes of pollutant emissions due to COVID-19 and associated governmental control measures is crucial to understand its impacts on economy, air pollution, and society. We used the WRF-GC model and the tropospheric NO2 column observations retrieved by the TROPOMI instrument to derive the top-down NOx emission change estimation between the three periods: P1 (January 1st to January 22nd, 2020), P2 (January 23rd, Wuhan lockdown, to February 9th, 2020), and P3 (February 10th, back-to-work day, to March 12th, 2020). We found that NOx emissions in East China averaged during P2 decreased by 50% compared to those averaged during P1. The NOx emissions averaged during P3 increased by 26% compared to those during P2. Most provinces in East China gradually regained some of their NOx emissions after February 10, the official back-to-work day, but NOx emissions in most provinces have not yet to return to their previous levels in early January. NOx emissions in Wuhan, the first epicenter of COVID-19, had no sign of emission recovering by March 12. A few provinces, such as Zhejiang and Shanxi, have recovered fast, with their averaged NOx emissions during P3 almost back to pre-lockdown levels.

China’s nationwide ozone monitoring network initiated in 2013 has observed severe surface ozone pollution. This network, combined with the recent Tropospheric Ozone Assessment Report (TOAR) data set, offers a more comprehensive view on global surface ozone distribution and trends. Here, we report quantitative estimates of the warm-season (April–September) surface ozone trends and resulting health impacts at Chinese cities in 2013–2019. Both the parametric and nonparametric linear trends for 12 ozone metrics relevant to human health and vegetation exposure are derived. We find that all ozone metrics averaged from Chinese urban sites have increased significantly since 2013. The warm-season daily maximum 8-h average (MDA8) ozone levels increased by 2.4 ppb (5.0%) year–1, with over 90% of the sites showing positive trends and 30% with trends larger than 3.0 ppb year–1. These rates are among the fastest trends, even faster in some Chinese cities, compared with the urban ozone trends in any other region worldwide reported in TOAR. Ozone metrics reflecting the cumulative exposure effect on human health and vegetation such as SOMO35 and AOT40 have increased at even faster rates (>10% year–1). We estimate that the total premature respiratory mortalities attributable to ambient MDA8 ozone exposure in 69 Chinese cities are 64,370 in 2019, which has increased by 60% compared to 2013 levels and requires urgent attention.

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The microbial cleavage of dimethylsulfoniopropionate (DMSP) generates volatile DMS through the action of DMSP lyases and is important in the global sulfur and carbon cycles. When released into the atmosphere from the oceans, DMS is oxidized, forming cloud condensation nuclei that may influence weather and climate. Six different DMSP lyase genes are found in taxonomically diverse microorganisms, and dddQ is among the most abundant in marine metagenomes. Here, we examine the molecular mechanism of DMSP cleavage by the DMSP lyase, DddQ, from Ruegeria lacuscaerulensis ITI_1157. The structures of DddQ bound to an inhibitory molecule 2-(N-morpholino)ethanesulfonic acid and of DddQ inactivated by a Tyr131Ala mutation and bound to DMSP were solved. DddQ adopts a β-barrel fold structure and contains a Zn 2+ ion and six highly conserved hydrophilic residues (Tyr120, His123, His125, Glu129, Tyr131, and His163) in the active site. Mutational and biochemical analyses indicate that these hydrophilic residues are essential to catalysis. In particular, Tyr131 undergoes a conformational change during catalysis, acting as a base to initiate the β-elimination reaction in DMSP lysis. Moreover, structural analyses and molecular dynamics simulations indicate that two loops over the substratebinding pocket of DddQ can alternate between "open" and "closed" states, serving as a gate for DMSP entry. We also propose a molecular mechanism for DMS production through DMSP cleavage. Our study provides important insight into the mechanism involved in the conversion of DMSP into DMS, which should lead to a better understanding of this globally important biogeochemical reaction.DMSP lyase DddQ | DMSP lyase structure | DMS generation | DMSP cleavage mechanism | marine bacteria T he compatible solute dimethylsulfoniopropionate (DMSP) is produced worldwide in a large amount, ∼10 9 tons per annum, mainly by marine phytoplankton and macroalgae; thus, this compound is a major participant in the global sulfur and carbon cycles (1, 2). Some DMSP is broken down by the algae producing it (3), but it is primarily catabolized by marine bacteria via two pathways, the demethylation pathway and the cleavage pathway (4). In the demethylation pathway, DMSP is demethylated and the methylmercaptopropionate generated is subsequently demethiolated to release methanthiol, providing the marine microbial food web a source of reduced sulfur (4). In the cleavage pathway, DMSP is cleaved by DMSP lyases to generate DMS, an environmentally important gas, and acrylate (or 3-hydroxypropionate) (5). DMS is the major form of biogenic sulfur that enters the atmosphere from the oceans (6). Some 300 Tg of DMS is annually produced by microbial activities, about 10% of which is transferred from oceans to the atmosphere (7,8). DMS in the atmosphere can be photochemically oxidized into DMSO or sulfate aerosols (9), which can scatter solar radiation directly and also form cloud condensation nuclei that influence the reflectivity of clouds and thereby global temperature (9, 10). These s...

BackgroundSevere fever with thrombocytopenia syndrome virus (SFTSV), which can cause hemorrhagic fever–like illness, is a newly discovered bunyavirus in China. The pathogenesis of SFTSV infection is poorly understood. However, it has been suggested that immune mechanisms, including cytokines and chemokines, play an important role in disease pathogenesis. In the present study, we investigated host cytokine and chemokine profiles in serum samples of patients with SFTSV infection from Northeast China and explored a possible correlation between cytokine levels and disease severity.Methods and Principal FindingsAcute phase serum samples from 40 patients, diagnosed with SFTSV infection were included. Patients were divided into two groups – severe or non-severe – based on disease severity. Levels of tumor necrosis factor (TNF)-α, transforming growth factor (TGF)-β, interleukin-6, interferon (IFN)-γ, IFN- γ-induced protein (IP)-10 and RANTES were measured in the serum samples with commercial ELISAs. Statistical analysis showed that increases in TNF-α, IP-10 and IFN-γ were associated with disease severity.ConclusionsWe suggest that a cytokine-mediated inflammatory response, characterized by cytokine and chemokine production imbalance, might be in part responsible for the disease progression of patients with SFTSV infection.