Environmental selection and evolutionary process jointly shape genomic and functional profiles of mangrove rhizosphere microbiomes

Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning.However,how such activities affect microbially driven methane(CH4),nitrogen(N),and sulfur(S)cycling of rhizosphere microbiomes remains unclear.To understand the effect of environmental selection and the evolutionary process on microbially driven biogeochemical cycles in native and introduced mangrove rhizospheres,we analyzed key genomic and functional profiles of rhizosphere microbiomes from native and introduced mangrove species by metagenome sequencing technologies.Compared with the native mangrove(Kandelia obovata,KO),the introduced mangrove(Sonneratia apetala,SA)rhizosphere microbiome had significantly(p<0.05)higher average genome size(AGS)(5.8 vs.5.5 Mb),average 16S ribosomal RNA gene copy number(3.5 vs.3.1),relative abundances of mobile genetic elements,and functional diversity in terms of the Shannon index(7.88 vs.7.84)but lower functional potentials involved in CH4 cycling(e.g.,mcrABCDG and pmoABC),N2 fixation(nifHDK),and inorganic S cycling(dsrAB,dsrC,dsrMKJOP,soxB,sqr,and fccAB).Similar results were also observed from the recovered Proteobacterial metagenome-assembled genomes with a higher AGS and distinct functions in the introduced mangrove rhizosphere.Additionally,salinity and ammonium were identified as the main environmental drivers of functional profiles of mangrove rhizosphere microbiomes through deterministic processes.This study advances our understanding of microbially mediated biogeochemical cycling of CH_(4),N,and S in the mangrove rhizosphere and provides novel insights into the influence of environmental selection and evolutionary processes on ecosystem functions,which has important implications for future mangrove reforestation.

Assessment of carbon sink potential and methane reduction scenarios of marine macroalgae(Gracilaria)cultivation

Marine macroalgae cultivation is an important part of the effort to address climate change through carbon sinks.Gracilaria,especially Gracilaria lemaneiformis and Gracilaria lichenoides are the major macroalgae cultivated in China.This study proposes a method to assess the net carbon sink of marine macroalgae(Gracilaria)cultivation.First,the net carbon sink of Gracilaria cultivation in China is calculated based on the yield of annual cultivated Gracilaria recorded in China Fishery Statistical Yearbook from 2011 to 2020.Next,we predict the net carbon sink trend of Gracilaria cultivation from 2021 to 2030 using the autoregressive integrated moving average model(ARIMA).Finally,the potential carbon sink increase and methane reduction related to Gracilaria cultivation in China is explored through a scenario analysis.We find that the net carbon sink of Gracilaria cultivation in China was about 32.1-92.4 kilotons per year from 2011 to 2020,and shows a great annual growth trend.Moreover,the predicted net carbon sink of Gracilaria cultivation would increase to 77.8-191.4 kilotons per year from 2021 to2030,thereby could contribute considerably in the achievement of China's carbon peak goal.Under a scenario of producing ruminant green feed with additional Gracilaria cultivation,each ton of macroalgae is predicted to reduce carbon emission(i.e.,methane)by 0.33-0.68 tons.Thus,marine macroalgae cultivation might form a synergistic chain of"carbon sink increase-water purification-economy-methane reduction".This study proposes a synergistic new model that operates through marine macroalgae cultivation,economic aquaculture,and green feed production.

Revealing the roles of TLR7, a nucleic acid sensor for COVID-19 in pan-cancer

Recent studies suggested that cancer was a risk factor for coronavirus disease 2019 (COVID-19). Toll-like receptor 7 (TLR7), a severe acute respiratory syndrome 2 (SARS-CoV-2) virus’’s nucleic acid sensor, was discovered to be aberrantly expressed in many types of cancers. However, its expression pattern across cancers and association with COVID-19 has not been systematically studied. In this study, we proposed a computational framework to comprehensively study the roles of TLR7 in COVID-19 and pan-cancers at genetic, gene expression, protein, epigenetic, and single-cell levels. We found TLR7 mRNA expression was significantly up-regulated in 6 cancer types and down-regulated in 6 cancer types, further validated in the HPA database at the protein level. The genes significantly co-expressed with TLR7 were mainly enriched in the toll-like receptor signaling pathway, endolysosome, and signaling pattern recognition receptor activity. In addition, the abnormal TLR7 expression was associated with Mismatch repair (MMR), microsatellite instability (MSI), tumor mutational burden (TMB) in various cancers. Mined by the ESTIMATE algorithm, the expression of TLR7 was also closely linked to various immune infiltration patterns in pan-cancer, and TLR7 was mainly enriched in macrophages, as revealed by single-cell RNA sequencing. Finally, TLR7 expressions were very sensitive to a few targeted drugs, such as Alectinib and Imiquimod. In conclusion, TLR7 might be essential in the pathogenesis of COVID-19 and cancers.

The Effects of Mindfulness-Based Interventions on Symptoms of Mild Traumatic Brain Injury:A Systematic Review

Mindfulness-based interventions(MBIs)are emerging non-pharmacological treatments for mild traumatic brain injury(mTBI).In this systematic review,the authors aimed to evaluate the potential efficacy of MBIs to provide recommendations for treating patients with mTBI.We searched of the English literature on MBIs for patients with mTBI as of 01 September,2023,using the PubMed,Web of Science,PsycINFO,and Scopus databases.One author performed data extraction and quality scoring of the included literature according to the proposed protocol,and another conducted the review.The review was not registered.A total of 11 studies met the final inclusion criteria,5 of which involved military personnel(veterans).MBIs covered in this review include goal-oriented attention self-regulation(GOALS),mindfulness-based stress reduction(MBSR),acceptance and commitment therapy(ACT),and so on.Research shows that MBSR mainly reduces mental fatigue symptoms in mTBI patients,and GOALS tend to improve their cognitive function.The effect of MBIs on psychological symptoms needs further exploration.Other studies,such as mindfulness-based group therapy and intervention studies targeting mTBI military personnel,are relatively sparse.MBIs have specific effects on mental fatigue and cognitive dysfunction in patients with mTBI.However,the effect on psychological distress and the sustained effectiveness across all symptoms still need further exploration.Considering the particularity of military personnel suffering from mTBI,researchers need to do more intervention studies targeting mTBI military personnel.Therefore,the design of future MBIs trials for mTBI patients’needs to take into account all the factors,such as different populations and severity of traumatic brain injury,to verify the effectiveness of MBIs in alleviating mTBI symptoms and explore the mechanism of intervention.

Occurrence of human pathogenic bacteria carrying antibiotic resistance genes revealed by metagenomic approach: A case study from an aquatic environment

Antibiotic resistance genes(ARGs), human pathogenic bacteria(HPB), and HPB carrying ARGs are public issues that pose a high risk to aquatic environments and public health. Their diversity and abundance in water, intestine, and sediments of shrimp culture pond were investigated using metagenomic approach. A total of 19 classes of ARGs, 52 HPB species, and 7 species of HPB carrying ARGs were found. Additionally, 157, 104, and 86 subtypes of ARGs were detected in shrimp intestine, pond water, and sediment samples, respectively. In all the samples, multidrug resistance genes were the highest abundant class of ARGs. The dominant HPB was Enterococcus faecalis in shrimp intestine, Vibrio parahaemolyticus in sediments, and Mycobacterium yongonense in water, respectively. Moreover, E. faecalis(contig Intestine_364647)and Enterococcus faecium(contig Intestine_80272) carrying efr A, efr B and ANT(6)-Ia were found in shrimp intestine, Desulfosaricina cetonica(contig Sediment_825143) and Escherichia coli(contig Sediment_188430) carrying mex B and APH(3′)-IIa were found in sediments, and Laribacter hongkongensis(contig Water_478168 and Water_369477), Shigella sonnei(contig Water_880246),and Acinetobacter baumannii(contig Water_525520) carrying sul1, sul2, ere A, qac H, OXA-21, and mph D were found in pond water. Mobile genetic elements(MGEs) analysis indicated that horizontal gene transfer(HGT) of integrons, insertion sequences, and plasmids existed in shrimp intestine, sediment, and water samples, and the abundance of integrons was higher than that of other two MGEs. The results suggested that HPB carrying ARGs potentially existed in aquatic environments, and that these contributed to the environment and public health risk evaluation.

Bacterial and eukaryotic community interactions might contribute to shrimp culture pond soil ecosystem at different culture stages

Sedimentary bacterial and eukaryotic communities are major components of the aquatic ecosystem.Revealing the linkages between their community structure and interactions is crucial to understand the diversity and functions of aquatic and soil ecosystems.However,how their diversity and assembly contribute to their interactions on time scale is unclear.This study examined sedimentary bacterial and eukaryotic communities in shrimp culture ponds at different culture stages.The most abundant bacteria were Proteobacteria(38.27%),whereas the most abundant eukaryotes were Chytridiomycota(27.48%).Bacterial and eukaryotic diversities were correlated(P<0.05),implying the strong interactions between bacteria and eukaryotes.Results showed that the bacterial and eukaryotic communities became increasingly similar on a local scale along with the shrimp culture.Only the eukaryotic community significantly increased in similarity along with the shrimp culture(P<0.05),suggesting that the sedimentary eukaryotic community structure is sensitive under shrimp culture.Co-occurrence network modeling indicated that positive microbial interactions were dominant.The homogeneous selection was the major driver of community assembly.Bacterial diversity negatively correlated with operational taxonomic units and positive links in networks(P<0.05),whereas eukaryotic diversities positively correlated with positive links in networks(P<0.05).This study broadens our knowledge about sedimentary microbial diversity,community assembly,and interaction patterns on time scale,providing a reference for the sustainable management in aquaculture production.