The increase of particle size shifts the biogeochemical cycle functions of mineral-associated microorganisms and weakens the mineral-associated organic carbon sink in mangrove soils.

Mineral-organic matter-microbe interactions greatly impact the biogeochemical processes and biodiversity in soils. An increasing trend of particle size (PS) in mangrove soils has been observed because of the relative sea level rise. However, the impacts of PS increase on the microbial biogeochemical functions and carbon sink in the mineral-associated microcosms are exceedingly nebulous. This work showed a remarkable difference in the communities of mineral-associated microorganisms (MMOs) in various PS fractions. Heavy metal contents and urease activity were the factors that mostly driven the MMO community variation in different PS fractions. Large PS fraction attenuated the stability of MMO communities according to the co-occurrence network characteristics. The PS increase significantly (P < 0.05) lowered the gene abundances for carbon input (e.g., carbon fixation) and raised the gene abundances for carbon loss (e.g., aerobic respiration). Combined with the significant decrease of mineral-associated organic carbon (MOC) in large PS fraction (P < 0.05), this work inferred that the PS increase could weaken the MOC sink partially due to the MMO function shift for carbon cycle. The current work indicated unhealthy changes of MMO communities and MOC storage in mangrove soils, and PS was of significance as an indicator for predicting the carbon sink function, especially for the stable form, such as MOC, in the soils of mangroves under the ecological background of climate migration. IMPORTANCE: Carbon with stable forms, such as mineral-associated organic carbon (MOC), is crucial for the sink capabilities in mangrove soils, and mineral-associated microorganisms (MMOs) are important players for the formation and metabolism of MOC. Therefore, the future successions of the MMO functions and MOC contents under the background of climate change are of value for a deeper understanding of mangrove ecology. The relative sea level rise caused by the global warming results in the increase of mangrove soil particle size (PS), which provides distinct microcosms for MMOs and MOC. However, the responses of MMO functions and MOC content to the PS increase of mangrove soils are unknown. The current study aims to reveal the succession regulations of MMO functions and their potential ecological impacts for the storages of MOC in different PS fractions, therefore widening our knowledge of future function migration and promoting the research development of mangrove.

Distinct Assembly Processes Structure Planktonic Bacterial Communities Among Near- and Offshore Ecosystems in the Yangtze River Estuary.

The estuarine system functions as natural filters due to its ability to facilitate material transformation, planktonic bacteria play a crucial role in the cycling of complex nutrients and pollutants within estuaries, and understanding the community composition and assembly therein is crucial for comprehending bacterial ecology within estuaries. Despite extensive investigations into the composition and community assembly of two bacterial fractions (free-living, FLB; particle-attached, PAB), the process by which bacterioplankton communities in these two habitats assemble in the nearshore and offshore zones of estuarine ecosystems remains poorly understood. In this study, we conducted sampling in the Yangtze River Estuary (YRE) to investigate potential variations in the composition and community assembly of FLB and PAB in nearshore and offshore regions. We collected 90 samples of surface, middle, and bottom water from 16 sampling stations and performed 16S rRNA gene amplicon analysis along with environmental factor measurements. The results unveiled that the nearshore communities demonstrated significantly greater species richness and Chao1 indices compared to the offshore communities. In contrast, the nearshore communities had lower values of Shannon and Simpson indices. When compared to the FLB, the PAB exhibit a higher level of biodiversity and abundance. However, no distinct alpha and beta diversity differences were observed between the bottom, middle, and surface water layers. The community assembly analysis indicated that nearshore communities are predominantly shaped by deterministic processes, particularly due to heterogeneous selection of PAB; In contrast, offshore communities are governed more by stochastic processes, largely due to homogenizing dispersal of FLB. Consequently, the findings of this study demonstrate that nearshore and PAB communities exhibit higher levels of species diversity, while stochastic and deterministic processes exert distinct influences on communities among near- and offshore regions. This study further sheds new light on our understanding of the mechanisms governing bacterial communities in estuarine ecosystems.

Agarose biodegradation by deep-sea bacterium Vibrio natriegens WPAGA4 with the agarases through horizontal gene transfer.

This study aimed to reveal the importance of horizontal gene transfer (HGT) for the agarose-degrading ability and the related degradation pathway of a deep-sea bacterium Vibrio natriegens WPAGA4, which was rarely reported in former works. A total of four agarases belonged to the GH50 family, including Aga3418, Aga3419, Aga3420, and Aga3472, were annotated and expressed in Escherichia coli cells. The agarose degradation products of Aga3418, Aga3420, and Aga3472 were neoagarobiose, while those of Aga3419 were neoagarobiose and neoagarotetraose. The RT-qPCR analysis showed that the expression level ratio of Aga3418, Aga3419, Aga3420, and Aga3472 was stable at about 1:1:1.5:2.5 during the degradation, which indicated the optimal expression level ratio of the agarases for agarose degradation by V. natriegens WPAGA4. Based on the genomic information, three of four agarases and other agarose-degrading related genes were in a genome island with a G + C content that was obviously lower than that of the whole genome of V. natriegens WPAGA4, indicating that these agarose-degrading genes were required through HGT. Our results demonstrated that the expression level ratio instead of the expression level itself of agarase genes was crucial for agarose degradation by V. natriegens WPAGA4, and HGT occurred in the deep-sea environment, thereby promoting the deep-sea carbon cycle and providing a reference for studying the evolution and transfer pathways of agar-related genes.

Parerythrobacter lacustris sp. nov., a novel member of the family Erythrobacteraceae isolated from an inland alpine lake.

A novel bacterium, designated as strain RS5-5T, was isolated from lake water in northwestern China. Cells of the isolate were observed to be rod shaped and Gram stain negative. Its growth occurred at 4-37 â„ƒ, pH 6.5-9.0 and in the presence of 0-5% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RS5-5T was most closely related to Qipengyuania sediminis GDMCC 1.2497T (97.5%), followed by Erythrobacter dokdonensis DSW-74T (97.3%) and Qipengyuania algicida GDMCC 1.2535T (97.0%). Phylogenomic analysis revealed that strain RS5-5T formed a distinct branch with the genus Parerythrobacter. The sole quinone was ubiquinone-10, and the major fatty acids (≥ 10%) were unsaturated fatty acids including C17:1 ω6c, summed feature 3 (C16:1 ω7c/C16:1 ω6c) and summed feature 8 (C18:1 ω7c/C18:1 ω6c). The polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, one unidentified sphingoglycolipid, three unidentified glycolipids, one unidentified aminoglycolipid, one unidentified aminolipid, two unidentified phospholipids and four unidentified polar lipids. Chemotaxonomic characteristics of strain RS5-5T were coincident with those of the genus Parerythrobacter members. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain RS5-5T and two Parerythrobacter reference strains were in the ranges of 73.2-77.7%, 69.0-78.0% and 18.9-20.4%, respectively. The genomic DNA G + C content of strain RS5-5T was 64.1%. The results of phenotypic, phylogenetic and genomic analyses suggested that strain RS5-5T represents a novel species in the genus Parerythrobacter, for which the name Parerythrobacter lacustris sp. nov. is proposed. The type strain is RS5-5T (= GDMCC 1.3163T = KCTC 92277T).

Aestuariibaculum lutulentum sp. nov., a marine bacterium isolated from coastal sediment in Beihai.

A Gram-stain negative, strictly aerobic, and rod-shaped bacterium, designated as strain L182T, was isolated from coastal sediment in Beihai, Guangxi Province, PR China. Colonies of strain L182T were yellow, 2 mm in diameter, round, opaque, smooth and convex after incubation on marine ager at 30 °C for 3 days. Cells were catalase-positive but oxidase-negative. Growth of strain L182T was observed at 4-40 °C (optimum, 25 °C), pH 5.5-10.0 (optimum, pH 5.5-8.0) and with 0-6% (w/v) NaCl (optimum, 0.5-4.0%). The G + C content based on the genome sequence was 36.0%. The only respiratory quinone was MK-6. The main polar lipids included phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid, one unidentified glycolipids, four unidentified aminolipids and six unidentified lipids. The major fatty acids (> 10%) were iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH. The 16S rRNA gene sequence similarity between strain L182T and Aestuariibaculum suncheonense SC17T was 98.2%, and the similarities with other type strains of the genus Aestuariibaculum were 96.1-97.2%. The average nucleotide identity and in silicon DNA-DNA hybridization values between the strain L182T and its closely related Aestuariibaculum species were 80.8-85.2% and 22.0-29.5%. According to the above results, Aestuariibaculum lutulentum sp. nov. was proposed as a novel species. The type strain is L182T (= MCCC 1K08065T = KCTC 92530T).

Parerythrobacter aestuarii sp. nov., Isolated from Seawater in the Tidal Region of Taizhou.

A yellow, Gram-stain-negative, aerobic, and rod-shaped strain, designated as C18T, was isolated from seawater in the tidal region of Taizhou. Growth of strain C18T occurs at 20-45 °C, at pH 5.5-8.0 and with 1.0-8.0% (w/v) NaCl. The 16S rRNA gene sequence analysis showed that strain C18T shared sequence identities with the genera Erythrobacter (< 98.4%), Qipengyuania (< 98.0%), Altererythrobacter (< 96.4%), Parerythrobacter (< 96.2%), Aurantiacibacter (< 96.2%), Tsuneonella (< 96.0%), Pelagerythrobacter (< 96.0%), Alteriqipengyuania (< 95.9%), and Parapontixanthobacter (< 95.7%) type strains. While the phylogenomic tree based on single-copy orthologous clusters revealed that strain C18T was stably clustered into the genus Parerythrobacter. Average nucleotide identity and digital DNA-DNA hybridization values of strain C18T and Parerythrobacter type strains were 73.5-75.2% and 18.5-19.4%, respectively, which were lower than the species delineation thresholds. The sole respiratory quinones were identified as ubiquinone-10. The major fatty acids (> 10%) were C17:1ω6c and summed feature 8 (C18:1ω7c and/or C18:1ω6c). Polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, an unidentified phospholipid, and an unidentified aminophospholipid. Based on the genetic, chemotaxonomic and phenotypic results, strain C18T is concluded to represent a novel species in the genus Parerythrobacter, for which the name Parerythrobacter aestuarii sp. nov. is proposed. The type strain is C18T (= KCTC 82594T = MCCC 1K05109T).

The importance of conditionally rare taxa for the assembly and interaction of fungal communities in mangrove sediments.

The fungal communities provide the nutrients and drive the cycles of elements in nature, and the rare fungal taxa are proved to be crucial for these communities in many environments. However, the ecological functions of rare taxa for the fungal communities in mangrove ecosystems are poorly assessed until now. This work aims to reveal the importance of rare taxa for the assembly of fungal communities in mangrove sediments by using the amplicon sequencing analysis of different spatiotemporal samples collected from Sanya mangroves, China. The results showed that Ascomycota and Basidiomycota were the dominant phyla in the conditionally rare taxa (CRT). The fungal communities possessed outstanding stability against the spatiotemporal variation and most collected environmental factors. The CRT possessed narrower niches and were more affected by the environmental variables than the abundant taxa. The current work demonstrated that the CRT had significantly higher relative abundances, degrees (the number of adjacent edges), clustering coefficients, and closeness centralities in the top 8 modules of the co-occurrence network (p < 0.05), indicating the important role of the CRT for the interaction of fungal communities in mangrove sediments. These findings indicate the importance of the CRT for the fungal community structures in mangrove sediments, and would deepen our understanding of dynamic functions of mangrove fungi, thereby facilitating the management, utilization, and protection of mangrove ecosystems. KEY POINTS: • Fungal communities in mangrove sediments are stable against environment variations. • The conditionally rare taxa (CRT) possessed narrower niches than the abundant fungal taxa. • The CRT are central for the co-occurrence network and interaction of fungal communities.

Agarose-Degrading Characteristics of a Deep-Sea Bacterium Vibrio Natriegens WPAGA4 and Its Cold-Adapted GH50 Agarase Aga3420.

Up until now, the characterizations of GH50 agarases from Vibrio species have rarely been reported compared to GH16 agarases. In this study, a deep-sea strain, WPAGA4, was isolated and identified as Vibrio natriegens due to the maximum similarity of its 16S rRNA gene sequence, the values of its average nucleotide identity, and through digital DNA-DNA hybridization. Two circular chromosomes in V. natriegens WPAGA4 were assembled. A total of 4561 coding genes, 37 rRNA, 131 tRNA, and 59 other non-coding RNA genes were predicted in the genome of V. natriegens WPAGA4. An agarase gene belonging to the GH50 family was annotated in the genome sequence and expressed in E. coli cells. The optimum temperature and pH of the recombinant Aga3420 (rAga3420) were 40 °C and 7.0, respectively. Neoagarobiose (NA2) was the only product during the degradation process of agarose by rAga3420. rAga3420 had a favorable stability following incubation at 10-30 °C for 50 min. The Km, Vmax, and kcat values of rAga3420 were 2.8 mg/mL, 78.1 U/mg, and 376.9 s-1, respectively. rAga3420 displayed cold-adapted properties as 59.7% and 41.2% of the relative activity remained at 10 3 °C and 0 °C, respectively. This property ensured V. natriegens WPAGA4 could degrade and metabolize the agarose in cold deep-sea environments and enables rAga3420 to be an appropriate industrial enzyme for NA2 production, with industrial potential in medical and cosmetic fields.

Characteristics and mechanism of heterotrophic nitrification/aerobic denitrification in a novel Halomonas piezotolerans strain.

A strain was isolated from an activated sludge system and identified as Halomonas piezotolerans HN2 in this study, which is the first strain in H. piezotolerans with the capability of heterotrophic nitrification and aerobic denitrification. Strain HN2 showed the maximum nitrogen removal rate of 9.10 mg/L/h by utilizing ammonium at the salinity of 3.0%. Under saline environment, HN2 could remove nitrogen efficiently in neutral and slightly alkaline environments, with the carbon sources of sodium succinate and sodium citrate and the C/N ratio of 15-20, and the maximum removal efficiencies of ammonium, nitrite, and nitrate were 100%, 96.35%, and 99.7%, respectively. The genomic information revealed the presence of amoA, napA, and nosZ genes in strain HN2, and the target bands of nirS were obtained via a polymerase chain reaction. Therefore, we inferred that ammonium was mainly utilized for the growth of strain HN2 through assimilation, and another part of the initial ammonium was converted into nitrate through nitrification, and then into gaseous nitrogen through denitrification. This report indicated the potential application of strain HN2 and other nitrifying and denitrifying Halomonas strains in the removal of nitrogen pollution in marine-related environments and also implies the important role of Halomonas in the nitrogen cycle process of the ocean.

Stochastic processes shape the aggregation of free-living and particle-attached bacterial communities in the Yangtze River Estuary, China.

An estuary plays an important role in material and energy exchange between the land and sea, where complex physical, chemical, and biological processes occur. Here, we investigated the assembly processes of free-living (FL) and particle-associated (PA) bacterial communities in two seawater layers at five stations in the Yangtze River Estuary (YRE) by using 16S rRNA sequencing methods. The results indicated that Proteobacteria was the most abundant phylum in the YRE. The α-diversity of PA community was significantly higher than FL community, and analysis of similarity showed significantly different (Global R = 0.2809, p < 0.005). RDA revealed that phosphate (PO4 3- ) was significantly correlated with PA bacterial community abundance (p < 0.05). An ecological null model showed that both PA and FL bacterial communities were mainly influenced by stochastic processes (PA: 100%, FL: 70%), which PA attached to nutrient particles and are less affected by environmental filtration. Dispersal limitation (50%) was the main assembly process of the PA community, while homogeneous selection (30%) and drift (30%) were important processes in the FL community assembly. The available substrate for colonization limits the transformation from FL to PA bacteria. This study would improve our understanding of FL and PA bacterial community structure and factors affecting assembly process in estuarine environments.

Complete genome sequence of Microbulbifer sp. YPW1 from mangrove sediments in Yanpu harbor, China.

In this work, a strain named YPW1 was isolated from the sediments of an artificial mangrove in Yanpu harbor, China. A complete genome of YPW1 was sequenced and assembled. The 16S rRNA gene assigned strain YPW1 into genus Microbulbifer, and the maximum values of average nucleotide identity and digital DNA-DNA hybridization of ZHDP1 genome were 90.36 and 68.1, respectively, indicating that YPW1 was a potential new species in genus Microbulbifer. A total of 10 representative genomes from genus Microbulbifer were selected to compare with YPW1. The results showed that the genome of strain YPW1 possessed more carbohydrate-active enzyme genes to transform various recalcitrant polysaccharides into bioavailable monosaccharides than those of the selected genomes. Furthermore, among the selected genomes, YPW1 was the only strain with nitrate, nitrite, and nitric oxide reductases which could appoint nitrous oxide, a powerful greenhouse gas, as the end-product of its denitrification process. Therefore, strain YPW1 was a potential novel member of genus Microbulbifer with special ecological roles in the cycles of carbon and nitrogen in mangrove ecosystems.

Vibrio ziniensis sp. nov., isolated from mangrove sediments.

A novel Gram-staining-negative, catalase- and oxidase-positive, facultatively anaerobic and rod-shaped motile bacterial strain, designated as ZWAL4003T, was isolated from mangrove sediments of the Zini Mangrove Forest, Zhangzhou City, PR China. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that ZWAL4003T was grouped into a separated branch with Vibrio plantisponsor MSSRF60T (97.38% nucleotide sequence identity) and Vibrio diazotrophicus NBRC 103148T (97.27%). The major cellular fatty acids were C14 : 0 (12.6%), C16 : 0 (17.6%), and summed feature 3 (C16 : 1ω6c /C16 : 1 ω7c, 45.6%). Its genome had a length of 4650556 bp with 42.8% DNA G+C content, and contained genes involved in the biosynthesis of bacteriocin, ß-lactone, resorcinol, N-acyl amino acid, and arylpolyene. The in silico DNA-DNA hybridization and average nucleotide identity values for whole-genome sequence comparisons between ZWAL4003T and V. plantisponsor LMG 24470T were clearly below the thresholds used for the delineation of a novel species. The morphological and chemotaxonomic characteristics and the genotypic data of ZWAL4003T indicated that it represented a novel species of the genus Vibrio. Its proposed name is Vibrio ziniensis sp. nov., and the type strain is ZWAL4003T (=KCTC 72971T=MCCC 1A17474T).

Expression and Characterization of a Novel Cold-Adapted and Stable ß-Agarase Gene agaW1540 from the Deep-Sea Bacterium Shewanella sp. WPAGA9.

The neoagaro-oligosaccharides, degraded from agarose by agarases, are important natural substances with many bioactivities. In this study, a novel agarase gene, agaW1540, from the genome of a deep-sea bacterium Shewanella sp. WPAGA9, was expressed, and the recombinant AgaW1540 (rAgaW1540) displayed the maximum activity under the optimal pH and temperature of 7.0 and 35 °C, respectively. rAgaW1540 retained 85.4% of its maximum activity at 0 °C and retained more than 92% of its maximum activity at the temperature range of 20-40 °C and the pH range of 4.0-9.0, respectively, indicating its extensive working temperature and pH values. The activity of rAgaW1540 was dramatically suppressed by Cu2+ and Zn2+, whereas Fe2+ displayed an intensification of enzymatic activity. The Km and Vmax of rAgaW1540 for agarose degradation were 15.7 mg/mL and 23.4 U/mg, respectively. rAgaW1540 retained 94.7%, 97.9%, and 42.4% of its maximum activity after incubation at 20 °C, 25 °C, and 30 °C for 60 min, respectively. Thin-layer chromatography and ion chromatography analyses verified that rAgaW1540 is an endo-acting ß-agarase that degrades agarose into neoagarotetraose and neoagarohexaose as the main products. The wide variety of working conditions and stable activity at room temperatures make rAgaW1540an appropriate bio-tool for further industrial production of neoagaro-oligosaccharides.

The degradation activities for three seaweed polysaccharides of Shewanella sp. WPAGA9 isolated from deep-sea sediments.

Seaweed oligosaccharides possess great bioactivities. However, different microbial strains are required to degrade multiple polysaccharides due to their limited biodegradability, thereby increasing the cost and complexity of production. Shewanella sp. WPAGA9 was isolated from deep-sea sediments in this study. According to the genomic and biochemical analyses, the extracellular fermentation broth of WPAGA9 had versatile degradation abilities for three typical seaweed polysaccharides including agar, carrageenan, and alginate. The maximum enzyme activities of the extracellular fermentation broth of WPAGA9 were 71.63, 76.4, and 735.13 U/ml for the degradation of agar, alginate, and carrageenan, respectively. Moreover, multiple seaweed oligosaccharides can be produced by the extracellular fermentation broth of WPAGA9 under similar optimum conditions. Therefore, WPAGA9 can simultaneously degrade three types of seaweed polysaccharides under similar conditions, thereby greatly reducing the production cost of seaweed oligosaccharides. This finding indicates that Shewanella sp. WPAGA9 is an ideal biochemical tool for producing multiple active seaweed oligosaccharides at low costs and is also an important participant in the carbon cycle process of the deep-sea environment.

Extracellular expression of agarase rAgaM1 in Bacillus subtilis and its ability for neoagaro-oligosaccharide production.

An agarase gene (agaM1) was cloned, expressed and characterized by using Escherichia coli as host strain, revealing the outstanding properties of recombinant AgaM1 (rAgaM1) in agarose degradation and neoagaro-oligosaccharides (NAs) production in our previous work. In current study, agaM1 was extracellularly expressed in Bacillus subtilis, and we aim to assess the ability of the supernatant of recombinant B. subtilis fermentation broth containing rAgaM1 to degrade agarose without protein purification, which would save the cost of purification and avoid the activity loss during purification. The pH and temperature optima for the supernatant were 7.0 and 50 °C, respectively. The supernatant containing rAgaM1 has outstanding stability against 40 °C and 50 °C. Besides, we detailedly studied the possible influence factors of rAgaM1 expression in the supernatant, including pH, temperature, isopropyl ß-D-thiogalactoside (IPTG) concentration, initial optical density at a wavelength of 600 nm (OD600 ), and induction time, and the optimum conditions for rAgaM1 expression by B. subtilis were confirmed. Moreover, the supernatant was able to produce NAs by using the Gracilaria lemaneiformis, whose cells were broken by autoclaving, as substrate, and a total of 1.41 µmol ml-1 of NA, including neoagarotetraose and neoagarohexaose, was produced after degradation for 48 h. This ability could save the cost of substrates in NA production, although the method requires a further study. Our results reveal that the NAs with great potential in food and pharmaceutical industries could be inexpensive to make by the supernatant containing rAgaM1 of B. subtilis fermentation broth in the foreseeable future.

Cloning, expression, and characterization of thermal-stable and pH-stable agarase from mangrove sediments.

AgaM1, a ß-agarase belonging to glycoside hydrolases family 16 (GH16), was cloned from the environmental DNA of mangrove sediments. The gene agaM1 is 2136 bp in length and encodes a protein of 712 amino acids. The properties of recombinant AgaM1 (rAgaM1) were studied using prokaryotic expression. The optimum temperature and pH were 50 °C and 7.0, respectively, and rAgaM1 exhibited a high adaptability to wide ranges of temperature and pH. A relatively high activity was retained at from 30 to 60 °C and from pH 6.0 to 9.0. Thermal stability was showed more than 70% relative activity after pre-incubation at 40 °C for 60 h. Outstanding pH stability were observed for rAgaM1 from pH 5.0 to 10.0 after pre-incubation for 60 h. Thin-layer chromatography revealed neoagarotetraose (NA4) and neoagarohexaose (NA6) were the end-products of rAgaM1-degraded agarose. Besides, rAgaM1 were found with a Km of 1.82 mg ml-1 and a Vm of 357.14 U mg-1 for agarose. The Km was smaller than those of most agarases reported previously. This discrepancy revealed the high affinity of rAgaM1 to agarose. Overall, the results indicated the potential of rAgaM1 in future industrial application.

Water masses influence the variation of microbial communities in the Yangtze River Estuary and its adjacent waters.

The Yangtze River estuary (YRE) are strongly influenced by the Kuroshio and terrigenous input from rivers, leading to the formation of distinct water masses, however, there remains a limited understanding of the full extent of this influence. Here the variation of water masses and bacterial communities of 58 seawater samples from the YRE and its adjacent waters were investigated. Our findings suggested that there were 5 water masses in the studied area: Black stream (BS), coastal water in the East China Sea (CW), nearshore mixed water (NM), mixed water in the middle and deep layers of the East China Sea (MM), and deep water blocks in the middle of the East China Sea (DM). The CW mass harbors the highest alpha diversity across all layers, whereas the NM mass exhibits higher diversity in the surface layer but lower in the middle layers. Proteobacteria was the most abundant taxa in all water masses, apart from that, in the surface layer masses, Cyanobacterium, Bacteroidota, and Actinobacteriota were the highest proportion in CW, while Bacteroidota and Actinobacteriota were the highest proportion in NM and BS; in the middle layer, Bacteroidota and Actinobacteriota were dominant phylum in CW and BS masses, but Cyanobacterium was main phylum in NM mass; in the bottom layer, Bacteroidota and Actinobacteriota were the dominant phylum in CW, while Marininimicrobia was the dominated phylum in DM and MM masses. Network analysis suggests water masses have obvious influence on community topological characteristics, moreover, community assembly across masses also differ greatly. Taken together, these results emphasized the significant impact of water masses on the bacterial composition, topological characteristics and assembly process, which may provide a theoretical foundation for predicting alterations in microbial communities within estuarine ecosystems under the influence of water masses.

Structure and assembly process of fungal communities in the Yangtze River Estuary.

Marine fungi are essential for the ecological function of estuarine ecosystems. However, limited studies have reported on the structure and assembly pattern of the fungal communities in estuaries. The purpose of this study is to reveal the structure and the ecological process of the fungal community in the Yangtze River Estuary (YRE) by using the amplicon sequencing method. Phyla of Ascomycota, Basidiomycota, and Chytridiomycota were dominant in the seawater and sediment samples from YRE. The null model analysis, community-neutral community model (NCM), and phylogenetic normalized stochasticity ratio (pNST) showed that the stochastic process dominated the assembly of fungal communities in YRE. Drift and homogeneous dispersal were the predominant stochastic processes for the fungal community assembly in seawater and sediment samples, respectively. The co-occurrence network analysis showed that fungal communities were more complex and closely connected in the sediment than in the seawater samples. Phyla Ascomycota, Basidiomycota, and Mucoromycota were the potential keystone taxa in the network. These findings demonstrated the importance of stochastic processes for the fungal community assembly, thereby widening our knowledge of the community structure and dynamics of fungi for future study and utilization in the YRE ecosystem.

Analogous assembly mechanisms and functional guilds govern prokaryotic communities in mangrove ecosystems of China and South America.

As an important coastal "blue carbon sink," mangrove ecosystems contain microbial communities with an as-yet-unknown high species diversity. Exploring the assemblage and structure of sediment microbial communities therein can aid in a better understanding of their ecosystem functioning, such as carbon sequestration and other biogeochemical cycles in mangrove wetlands. However, compared to other biomes, the study of mangrove sediment microbiomes is limited, especially in diverse mangrove ecosystems at a large spatial scale, which may harbor microbial communities with distinct compositions and functioning. Here, we analyzed 380 sediment samples from 13 and 8 representative mangrove ecosystems, respectively, in China and South America and compared their microbial features. Although the microbial community compositions exhibited strong distinctions, the community assemblage in the two locations followed analogous patterns: the assemblages of the entire community, abundant taxa, rare taxa, and generalists were predominantly driven by stochastic processes with significant distance-decay patterns, while the assembly of specialists was more likely related to the behaviors of other organisms in or surrounding the mangrove ecosystems. In addition, co-occurrence and topological network analysis of mangrove sediment microbiomes underlined the dominance of sulfate-reducing prokaryotes in both the regions. Moreover, we found that more than 70% of the keystone and hub taxa were sulfate-reducing prokaryotes, implying their important roles in maintaining the linkage and stability of the mangrove sediment microbial communities. This study fills a gap in the large-scale analysis of microbiome features covering distantly located and diverse mangrove ecosystems. Here, we propose a suggestion to the Mangrove Microbiome Initiative that 16S rRNA sequencing protocols should be standardized with a unified primer to facilitate the global-scale analysis of mangrove microbiomes and further comparisons with the reference data sets from other biomes.IMPORTANCEMangrove wetlands are important ecosystems possessing valuable ecological functions for carbon storage, species diversity maintenance, and coastline stabilization. These functions are greatly driven or supported by microorganisms that make essential contributions to biogeochemical cycles in mangrove ecosystems. The mechanisms governing the microbial community assembly, structure, and functions are vital to microbial ecology but remain unclear. Moreover, studying these mechanisms of mangrove microbiomes at a large spatial scale can provide a more comprehensive insight into their universal features and can help untangle microbial interaction patterns and microbiome functions. In this study, we compared the mangrove microbiomes in a large spatial range and found that the assembly patterns and key functional guilds of the Chinese and South American mangrove microbiomes were analogous. The entire communities exhibited significant distance-decay patterns and were strongly governed by stochastic processes, while the assemblage of specialists may be merely associated with the behaviors of the organisms in mangrove ecosystems. Furthermore, our results highlight the dominance of sulfate-reducing prokaryotes in mangrove microbiomes and their key roles in maintaining the stability of community structure and functions.

The first complete genome sequence of Microbulbifer celer KCTC12973T, a type strain with multiple polysaccharide degradation genes.

Genus Microbulbifer plays important roles in element cycling process in marine environments, and the first type strain KCTC 12973T (=ISL-39T = CCUG 54356T) of M. celer was isolated and identified in 2007. However, the genome sequence of M. celer KCTC 12973T is still unclear, which complicates the functional exploration and new species identification of other species belonged to this genus. This study reported the complete genome sequence of M. celer KCTC 12973T with a genome size of 4,346,001 bp. A total of 3601 protein-coding genes were annotated in the genome. The potential genes involved in the polysaccharide degradation, including cellulose, chitin, xylan, and pectate, were found in the protein-coding genes. Besides, the reductase genes of nitrate and nitrite were also annotated in the genome. These findings indicated the potential crucial ecological functions of M. celer KCTC 12973T for carbon and nitrogen cycles in marine ecosystems.