Devosia aquimaris sp. nov., isolated from seawater of the Changjiang River estuary of China.

A gram-stain-negative, aerobic, rod-shaped bacterium strain CJK-A8-3T was isolated from a polyamine-enriched seawater sample collected from the Changjiang River estuary of China. The colonies were white and circular. Strain CJK-A8-3T grew optimally at 35 °C, pH 7.0 and 1.5% NaCl. Its polar lipids contained phosphatidylglycerol, phosphatidic acid, unidentified glycolipids, and a combination of phospholipids and glycolipids. The respiratory quinone was ubiquinone-10, and its main fatty acids were C16:0, 11-methyl C18:1ω7c and Summed Feature 8 (including C18:1ω7c/C18:1ω6c). The phylogenetic tree based on 16S rRNA genes placed strain CJK-A8-3T in a new linage within the genus Devosia. 16S rRNA gene sequence of strain CJK-A8-3T showed identities of 98.50% with Devosia beringensis S02T, 98.15% with D. oryziradicis, and 98.01% with D. submarina JCM 18935T. The genome size of strain CJK-A8-3T was 3.81 Mb with the DNA G + C content 63.9%, higher than those of the reference strains (60.4-63.8%). The genome contained genes functional in the metabolism of terrigenous aromatic compounds, alkylphosphonate and organic nitrogen, potentially beneficial for nutrient acquirement and environmental remediation. It also harbored genes functional in antibiotics resistance and balance of osmotic pressure, enhancing their adaptation to estuarine environments. Both genomic investigation and experimental verification showed that strain CJK-A8-3T could be versatile and efficient to use diverse organic nitrogen compounds as carbon and nitrogen sources. Based on phenotypic, chemotaxonomic, phylogenetic and genomic characteristics, strain CJK-A8-3T was identified as a novel Devosia species, named as Devosia aquimaris sp. nov. The type strain is CJK-A8-3T (= MCCC 1K06953T = KCTC 92162T).

Rheinheimera oceanensis sp. nov., a novel member of the genus Rheinheimera, isolated from the West Pacific Ocean.

Two Gram-stain-negative, aerobic, non-motile and short-rod-shaped bacteria, designated as strains GL-53T and GL-15-2-5, were isolated from the seamount area of the West Pacific Ocean and identified using a polyphasic taxonomic approach. The growth of strains GL-53ᵀ and GL-15-2-5 occurred at pH 5.5-10.0, 4-40 °C (optimum at 28 °C) and 0-10.0 % NaCl concentrations (optimum at 0-5.0 %). On the basis of 16S rRNA gene sequence analysis, strains GL-53ᵀ and GL-15-2-5 exhibited the highest similarity to Rheinheimera lutimaris YQF-2T (98.4 %), followed by Rheinheimera pacifica KMM 1406T (98.1 %), Rheinheimera nanhaiensis E407-8T (97.4 %), Rheinheimera aestuarii H29T (97.4 %), Rheinheimera hassiensis E48T (97.2 %) and Rheinheimera aquimaris SW-353T (97.2 %). Phylogenetic analysis revealed that the isolates were affiliated with the genus Rheinheimera and represented an independent lineage. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The sole isoprenoid quinone was ubiquinone 8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid (and one unidentified glycolipid. The DNA G+C content was 48.5 mol%. The average nucleotide identity, average amino acid identity and in silico DNA-DNA hybridization values among the genomes of strain GL-53ᵀ and the related strains in the genus Rheinheimera were 75.5-90.1 %, 67.5-93.9 % and 21.4-41.4 %, respectively. Based on their phenotypic, chemotaxonomic and genotypic properties, the two strains were identified as representing a novel species of the genus Rheinheimera, for which the name Rheinheimera oceanensis sp. nov. is proposed. The type strain is GL-53T (=KCTC 82651T=MCCC M20598T).

Preliminary assessment of carbonic acid dissociation constants: Insights from observations in China's east coastal oceans.

Based on observations in China's east coastal oceans, we conducted a preliminary assessment of 16 sets of carbonic acid dissociation constants (K1* and K2*) by comparing spectrophotometrically measured pH values at 25 °C with those calculated from total alkalinity and dissolved inorganic carbon. We obtained that K1* and K2* often performed differently within different salinity ranges, and that the constants of Millero et al. (2002) (M02) demonstrated the best performance for the salinity range of 24-35. In contrast, the often recommended constants of Mehrbach et al. (1973) refit by Dickson and Millero (1987) (DM87-M) and Lucker et al. (2000) (L00) would underestimate pH at salinities of 24-30. This was mainly associated with the higher product of K1* and K2* by DM87-M and L00 than by M02 at this salinity range. Also, we found almost no differences between pH values calculated with DM87-M and L00.

Wastewater inputs reduce the CO2 uptake by coastal oceans.

Every year a large quantity of wastewater is generated worldwide, but its influence on the carbon dioxide (CO2) uptake by coastal oceans is not well understood. Here, sea surface CO2 partial pressure (pCO2) and air-sea CO2 flux were examined in the Jiaozhou Bay (JZB), a temperate coastal bay strongly disturbed by wastewater inputs. Monthly surveys from April 2014 through March 2015 showed that surface pCO2 in the JZB substantially varied both temporally and spatially between 163 µatm and 1222 µatm, with an annual average of 573 µatm. During April-December, surface pCO2 was oversaturated with respect to the atmosphere, with high values exceeding 1000 µatm in the northeastern part of the bay, where seawater salinity was low mainly due to the inputs of wastewater with salinity close to zero. During January-March, surface pCO2 was undersaturated, with the lowest value of <200 µatm also mainly in the northeastern part because of low water temperature and strong biological production. Over an annual cycle, apparently sea surface temperature dominated the monthly variation of surface pCO2 in this shallow bay, while wastewater inputs and related biological production/respiration dominated its spatial variability. Overall, the JZB was a net CO2 source to the atmosphere, emitting 9.6 ± 10.8 mmol C m-2 d-1, unlike its adjacent western part of the Yellow Sea and most of the temperate coastal oceans which are a net CO2 sink. This was possibly associated with wastewater inputs that cause high sea surface pCO2 via direct inputs of CO2 and degradation of organic matter. Thus, from this viewpoint reducing wastewater discharge or lowering CO2 levels in discharged wastewater may be important paths to enhancing the CO2 uptake by coastal oceans in the future.

Parkin increases the risk of colitis by downregulation of VDR via autophagy-lysosome degradation.

Parkin, an E3 ubiquitin ligase, plays an essential role in mitophagy. Emerging evidence indicates that mitophagy is involved in various processes closely related to immune diseases, including inflammatory bowel diseases (IBD). Here, the authors show that Parkin increases the occurrence of colitis and severe inflammation. Deletion of Parkin resulted in marked reductions in colonic inflammation and exhibited high resistance to DSS-induced colitis. Mechanism investigation indicated that Parkin interacts with Vitamin D receptors (VDR), a critical inhibitory regulator in IBD. Parkin promotes VDR degradation via the p62-related autophagy-lysosome pathway. Comparison of colitis in Parkin-/- and Parkin-/-Vdr-/- mice showed that the protective effect of Parkin deletion against colitis was abolished by VDR deletion. The result suggests that the regulatory effect of Parkin in colitis is a VDR-dependent pathway. Our research provides a new role of Parkin in colitis by downregulating VDR, which provides a potential strategy for treating IBD.

Microelectrode characterization of coral daytime interior pH and carbonate chemistry.

Reliably predicting how coral calcification may respond to ocean acidification and warming depends on our understanding of coral calcification mechanisms. However, the concentration and speciation of dissolved inorganic carbon (DIC) inside corals remain unclear, as only pH has been measured while a necessary second parameter to constrain carbonate chemistry has been missing. Here we report the first carbonate ion concentration ([CO3(2-)]) measurements together with pH inside corals during the light period. We observe sharp increases in [CO3(2-)] and pH from the gastric cavity to the calcifying fluid, confirming the existence of a proton (H(+)) pumping mechanism. We also show that corals can achieve a high aragonite saturation state (Ωarag) in the calcifying fluid by elevating pH while at the same time keeping [DIC] low. Such a mechanism may require less H(+)-pumping and energy for upregulating pH compared with the high [DIC] scenario and thus may allow corals to be more resistant to climate change related stressors.