Characterisation of the Bacteria and Archaea Community Associated with Wild Oysters, At Three Possible Restoration Sites in the North Sea

With 85% of the global oyster reefs destroyed, there is an urgent need for large scale restoration to benefit from the ecosystem services provided by biogenic oyster reefs and their associated biodiversity, including microorganisms that drive marine biogeochemical cycles. This experiment established a baseline for the monitoring of the bacterial and archaeal community associated with wild oysters, using samples from their immediate environment of the Voordelta, with cohabiting Crassostrea gigas and Ostrea edulis, Duikplaats with only C. gigas attached to rocks, and the Dansk Skaldyrcentre, with no onsite oysters. The microbial profiling was carried out through DNA analysis of samples collected from the surfaces of oyster shells and their substrate, the sediment and seawater. Following 16S rRNA amplicon sequencing and bioinformatics, alpha indices implied high species abundance and diversity in sediment but low abundance in seawater. As expected, Proteobacteria, Bacteroidetes, Firmicutes and Thaumarchaeota dominated the top 20 OTUs. In the Voordelta, OTUs related to Colwellia, Shewanella and Psychrobium differentiated the oysters collected from a reef with those attached to rocks. Duikplaats were distinct for sulfur-oxidizers Sulfurimonas and sulfate-reducers from the Sva 0081 sediment group. Archaea were found mainly in sediments and the oyster associated microbiome, with greater abundance at the reef site, consisting mostly of Thaumarchaeota from the family Nitrosopumilaceae. The oyster free site displayed archaea in sediments only, and algal bloom indicator microorganisms from the Rhodobacteraceae, Flavobacteriaceae family and genus [Polaribacter] huanghezhanensis, in addition to the ascidian symbiotic partner, Synechococcus. This study suggests site specific microbiome shifts, influenced by the presence of oysters and the type of substrate.

Linking bacterial and archaeal community dynamics to related hydrological,geochemical and environmental characteristics between surface water and groundwater in a karstic estuary

Subterranean estuaries(STEs)are characterized by the mixing of terrestrial fresh groundwater and seawater in coastal aquifers.Although microorganisms are important components of coastal groundwater ecosystems and play critical roles in biogeochemical transformations in STEs,limited information is available about how their community dynamics interact with hydrological,geochemical and environmental characteristics in STEs.Here,we studied bacterial and archaeal diversities and distributions with 16S rRNA-based Illumina MiSeq sequencing technology between surface water and groundwater in a karstic STE.Principal-coordinate analysis found that the bacterial and archaeal communities in the areas where algal blooms occurred were significantly separated from those in other stations without algal bloom occurrence.Canonical correspondence analysis showed that nutrients and salinity can explain the patterns of bacterial and archaeal community dynamics.The results suggest that hydrological,geochemical and environmental characteristics between surface water and groundwater likely control the bacterial and archaeal diversities and distributions in STEs.Furthermore,we found that some key species can utilize terrestrial pollutants such as nitrate and ammonia in STEs,indicating that these species(e.g.,Nitrosopumilus maritimus,Limnohabitans parvus and Simplicispira limi)may be excellent candidates for in situ degradation/remediation of coastal groundwater contaminations concerned with the nitrate and ammonia.Overall,this study reveals the coupling relationship between the microbial communities and hydrochemical environments in STEs,and provides a perspective of in situ degradation/remediation for coastal groundwater quality management.

Comparison of rumen archaeal diversity in adult and elderly yaks(Bos grunniens)using 16S rRNA gene high-throughput sequencing

This study was conducted to investigate the phylogenetic diversity of archaea in the rumen of adult and elderly yaks. Six domesticated female yaks, 3 adult yaks （（5.3±0.6） years old）, and 3 elderly yaks （（10.7±0.6） years old）, were used for the rumen contents collection. Illumina MiSeq high-throughput sequencing technology was applied to examine the archaeal composition of rumen contents. A total of 92 901 high-quality archaeal sequences were analyzed, and these were assigned to 2 033 operational taxonomic units （OTUs）. Among these, 974 OTUs were unique to adult yaks while 846 OTUs were unique to elderly yaks; 213 OTUs were shared by both groups. At the phylum level, more than 99% of the obtained OTUs belonged to the Euryarchaeota phylum. At the genus level, the archaea could be divided into 7 archaeal genera. The 7 genera （i.e., Methanobrevibacter, Methanobacterium, Methanosphaera, Thermogymnomonas, Methanomicrobiu, Meth- animicrococcus and the unclassified genus） were shared by all yaks, and their total abundance accounted for 99% of the rumen archaea. The most abundant archaea in elderly and adult yaks were Methanobrevibacterand Thermogymnomonas, respectively. The abundance of Methanobacteria （class）, Methanobacteriales （order）, Methanobacteriaceae （family）, and Methanobrevibacter （genus） in elderly yaks was significantly higher than in adult yaks. In contrast, the abundance of Ther-mogymnomonas in elderly yaks was 34% lower than in adult yaks, though the difference was not statistically significant. The difference in abundance of other archaea was not significant between the two groups. These results suggested that the structure of archaea in the rumen of yaks changed with age. This is the first study to compare the phytogenetic differences of rumen archaeal structure and composition using the yak model.

Weaning methods affect ruminal methanogenic archaea composition and diversity in Holstein calves

The objective of the present study was to examine the effect of different weaning methods on the ruminal methanogenic archaea composition and diversity in Holstein calves.Thirty-six newborn Holstein bull calves were assigned to 1 of 3 treatments:(1)conventional weaning(d 56)and fed a high proportion of solid feed(CWS);(2)conventional weaning(d 56)and fed a high proportion of liquid feed(CWL);(3)early weaning(d 42)and fed with a high proportion of solid feed(EWS).High-throughput sequencing of the methyl coenzyme M reductase(mcr A)gene,which encodes theα-subunit of methyl coenzyme M reductase-the enzyme that catalyzes the final step in methanogenesis was used to determine the composition and diversity of rumen methanogens.No significant difference(P>0.05)was observed for operational taxonomic units(OTUs)or richness indices,but diversity indices increased(P<0.05)for calves fed high dietary solids.Predominant families across the three treatments were Methanobacteriaceae,Thermoplasmataceae and Methanomassiliicoccaceae.Calves in the EWS treatment had a higher(P<0.05)relative abundance of Methanobrevibacter sp.strain AbM4 and Methanosphaera stadtmanae,while calves in the CWL treatment had a higher(P<0.05)abundance of Methanosphaera sp.strain SM9.A positive(P<0.05)relationship was identified between butyrate and Methanobrevibacter sp.strain AbM4.In conclusion,the composition and diversity of methanogens in the rumen of Holstein calves varied under the different weaning methods.This study identified a positive relationship between butyrate and Methanobrevibacter sp.strain AbM4,potentially reflecting correlations between ruminal fermentation variables and methanogenesis function.These in-depth analyses provide further understanding of weaning methods for intensified production systems.

Comparison of Fecal Methanogenic Archaeal Community Between Erhualian and Landrace Pigs Using Denaturing Gradient Gel Electrophoresis and Real-Time PCR Analysis

Erhualian and Landrace breeds are typical genetically obese and lean pigs, respectively. To compare the fecal methanogenic Archaeal community between these two pig breeds, fecal samples from different growth phase pigs were collected and used for PCR-denaturing gradient gel electrophoresis （DGGE） with two primer pairs （344fGC/519r and 519f/915rGC） and real-time PCR analysis. Results showed that a better separation and higher quality of bands pattern were obtained in DGGE proifles using primers 344fGC/519r as compared with primers 519f/915rGC. Sequencing of DGGE bands showed that the predominant methanogens in the feces of Erhualian and Landrace pigs belonged to Methanobrevibacter spp. and Methanosphaera spp. Real-time PCR analysis revealed that there was no signiifcant difference in the numbers of fecal total methanogens between Erhualian and Landrace pigs;however, pig growth phase affected the numbers of 16S rRNA genes of total methanogens and Methanobrevibacter smithii. Dissociation curves of methyl coenzyme-M reductase subunit A （mcrA） gene fragments ampliifed with real-time PCR showed all samples possessed a single peak at 82＆#176;C, which might be associated with M. smithii. Samples from the same growth phase of each breed showed good replicative dissociation curves. The results suggest that the growth phase （including diet factor） other than genotype of pig may affect the fecal methanogenic Archaeal community of pigs.

Shifts in community structure and function of ammoniaoxidizing archaea in biological soil crusts along a revegetation chronosequence in the Tengger Desert

Metagenomic studies have demonstrated the existence of ammonia-oxidizing archaea(AOA) and revealed they are responsible for ammoxidation in some extreme environments. However, the changes in compositional structure and ammonia-oxidation capacity of AOA communities in biological soil crusts(BSCs) of desert ecosystems remain poorly understood.Here, we utilized Illumina MiSeq sequencing and microbial functional gene array(GeoChip 5.0) to assess the above changes along a 51-year revegetation chronosequence in the Tengger Desert, China. The results showed a significant difference in AOA-community richness between 5-year-old BSCs and older ones. The most dominant phylum during BSC development was Crenarchaeota, and the corresponding species were ammonia-oxidizing_Crenarchaeote and environmental_samples_Crenarchaeota. Network analysis revealed that the positive correlations among dominant taxa increased, and their cooperation was reinforced in AOA communities during BSC succession. Redundancy analysis showed that the dominant factor influencing the change in AOA-community structure was soil texture. GeoChip 5.0 indicated that the amoA gene abundances of AOA and ammonia-oxidizing bacteria(AOB) were basically the same, demonstrating that AOA and AOB played an equally important role during BSCs development. Our study of the long-term succession of BSC demonstrated a persistent response of AOA communities to revegetation development in desert ecosystems.

Expression of mitogen-activated protein kinase double-stranded RNA in cucumber has no apparent effect on the diversity of rhizosphere archaea

The expression of mitogen-activated protein kinase （mapk） double-stranded RNA in cucumber is effective in controlling infestations of the root-knot nematode Meloidogyne incognita. However, little is known about the ecological effects of transgenic plants. Here, we analyzed the diversity of 16S rDNA genes derived from the rhizosphere archaea of transgenic cucumber plants as an indicator of ecological change. A total of 17 and 18 operational taxonomic units were detected in the rhizospheres of non-transgenic cucumber and mapk dsRNA-expressing plants, respectively. No significant difference was observed between the two groups according to Shannon and Simpson indices. In soil samples of the two rhizospheres, the dominant group was Crenarchaeota at the phylum level, with Staphylothermus, Methanococcus, Pyrodictium and Sulfolobus the abundant taxa at the genus level. These results suggest that expressing mapk double-stranded （ds） RNA in cucumber has no apparent effect on the diversity of rhizosphere archaea, and provide powerful evidence for the ecological safety of transgenic cucumber expressing mapk dsRNA.

Archaeal diversity and abundance within different layers of summer sea-ice and seawater from Prydz Bay,Antarctica

Fluorescence in-situ hybridization （FISH） and 16S rRNA gene clone library analyses were used to determine the abundance and diversity of archaea in Prydz Bay, Antarctica. Correlation analysis was also performed to assess links between physicochemical parameters and archaeal abundance and diversity within the sea-ice. Samples of sea-ice and seawater were collected during the 26th Chinese National Antarctic Research Expedition. The results of FISH showed that archaea were relatively abundant within the top layer of the sea-ice, and correlation analysis suggested that the concentration of 4NH＋ might be one of the main factors underlying this distribution pattern. However, using 16S rRNA gene libraries, archaea were not detected in the top and middle layers of the sea-ice. All archaeal clones obtained from the bottom layer of the sea-ice were grouped into the Marine Group I Crenarchaeota while the archaeal clones from seawater were assigned to Marine Group I Crenarchaeota, Marine Group II Euryarchaeota, and Marine Group III Euryarchaeota. Overall, the ifndings of this study showed that the diversity of archaea in the sea-ice in Prydz Bay was low.

Alteration of Intestinal Archaeal Community Composition in Broilers with Different Growth Rates

The gastrointestinal tract, as the major digestive and absorbing organ, plays an important role in chicken growth. Numerous studies have been undertaken to investigate the gut bacterial community in broilers, but little is known about the archaeal community composition. To improve our understanding of the composition of intestinal archaea and the relationship between archaea and chicken growth, a feeding trial was conducted with 10 000 Ross 308 chicks in a commercial production facility under standard management. At 38 d of age, 15 birds with the highest body weight （ H group）, 15 birds with average body weight （ M group）, and 15 birds with the lowest body weight （ L group） were selected among 600 healthy male individuals. Cecal archaeal community was detected based on 16S rRNA gene sequencing. As a result, 3 321 229 archaeal sequences were clustered into 1 281 operational taxonomic units （OTUs） and classified into three phyla （Crenarchaeola, Euryarchaeota and Thaumarchaeota） and six known genera ： Natronomonas, Halolamina, Salinarchaeum, Cenarchaeum, Candidatus, Nitrosoarchaeum and Nitrososphaera. The alpha indices showed that, the richness of archaea in L group was the highest, and followed by that in M group and H group, while the archaea in H group were more diverse, followed by those in M group and L group. However, the archaeal composition in all chicken samples was similar, with the vast majority of the sequences belonging to Cenarchaeum, and only a few belonging to the other five genera.

Bacterial and archaeal communities in deep sea waters near the Ninetyeast Ridge in Indian Ocean

Depth-dependent distribution patterns of bacterial and archaeal communities in deep sea water column around the Ninetyeast Ridge in the Indian Ocean were investigated using 16S rRNA gene profiling.Sampling was conducted at the northern Ninetyeast Ridge(1°59.89′N–9°59.70′S,87°58.90′E–88°00.03′E)from September to November 2016 where samples were collected from the bathyal(1000 m)to bathypelagic depths(>4000 m)in four different stations.A total of 1565405 clean data falling into 6712 bacterial OTUs and 1452727 clean data falling into 806 archaeal OTUs based on 97%similarity level were analyzed.Most of the bacterial 16S rRNA gene sequences were affiliated with Gammaproteobacteria,followed by Alphaproteobacteria and Bacteroidia.The archaeal 16S rRNA gene sequences mostly affiliated to Nitrososphaeria(Thaumarchaeota)dominated with relative abundances ranging from 52.68%to 97.2%,followed by Thermoplasmata(Euryarchaeota).Vertical partitioning of bacterial and archaeal communities among different water layers was observed.Canonical correspondence analysis(CCA)and Spearman’s correlations revealed that depth(P=0.003),dissolved oxygen(P=0.019),and nitrite(P=0.033)were the main environmental factors affecting bacterial community structure at genus level in the Ninetyeast Ridge.On the other hand,the first two CCA axes accounted for 74.4%of the explained total variance,it seems that the archaeal communities at genus level were heavily influenced by the environmental variables including depth,dissolved oxygen(DO),nitrite,salinity,phosphate,ammonia,nitrate,and silicate,but none of them exhibited any significant correlation on the structuring(P>0.1).

The Archaea Community Associated with Lava-Formed Gotjawal Forest Soil in Jeju, Korea

The abundance and diversity of archaeal assemblages were analyzed in soils collected from Gyorae Gotjawal forest, Jeju, Korea. Gotjawal soil refers to soil derived from a lava-formed forest, characterized by high organic matter content, fertility, and poor rocky soil. Using domain-specific primers, archaeal 16S rRNA gene sequences were PCR amplified for clone library construction, and a total of 185 archaeal clones were examined. The archaeal clones were affiliated with the phyla Thaumarchaeota (96.2%) and Euryarchaeota (3.8%). The most abundant thaumarchaeal group (90.3% of the clones) was the group I.1b clade, which includes soil ammonia-oxidizing archaea. The unique characteristics of Gotjawal soil, including basalt morphology, vegetation, and groundwater aquifer penetration, may be reflected in the archaeal community composition. Further study is necessary to understand the unique factors of Gotjawal soils that influence archaeal abundance, composition, and diversity.

Archaea Diversity of Five Hot Springs in Lushan from Henan

There are five hot springs named separately SHANGT,ZHONGT,WENT,XIAT and SHENT in Lushan County,Pingdingshan City,Henan Province.The archaeal diversity of the five hot springs was investigated and analyzed.16 S rD NA v4-5 genes of archaea were sequenced by Illumina Hisiq2500 PE250 technology.The numbers of sample sequences and OTUs were sorted by using Uparse,Mothur,SILVA,MUSCLE and Qiime software.Finally,the archaeal abundance and diversity in the five hot springs were analyzed.87993,67326,44400,48611 and 48495 effective reads have been obtained from SHANGT,ZHONGT,WENT,XIAT and SHENT respectively,and 520,280,678,451 and 437 OTUs have been acquired.The analysis of archaeal classification showed that the archaea from the five hot springs could be classified into 11 phyla,in which Thaumarchaeota accounted for 95.25%and was the dominant archaea.In the genera level,the dominant archaea of the SHANGT,ZHONGT and WENT was Candidatus-Nitrosocaldus,and unidentified-Thaumarchaeota was the dominant archaea in XIAT and SHENT.The results showed that the five hot springs in Lushan are rich in microbial resources.The research provided basic data for further research and utilization of the archaea resources in the five hot springs of Lushan.

Isolation and characterization of halophilic bacteria and archaea from salt ponds in Hangu Saltworks, Tianjin, China

A total of 26 isolates were obtained from solar salt ponds of different salinities(100, 150, 200, and 250) in Hangu Saltworks Co. Ltd., Tianjin, China. Phylogenetic analysis of 16 SrRNA gene sequences indicated that five bacteria genera H alomonas, Salinicoccus, Oceanobacillus, Gracibacillus, and Salimicrobium and one archaea genera H alorubrum were present. The genus H alomonas was predominant with eight strains distributed in a salinity range of 100–200, followed by H alorubrum with six strains in salinity 250. Based on the genus and original sampling salinity, eight bacterial and two archaeal isolates were selected for further morphological, physiological, and biochemical characterization. All of the bacterial strains were moderately halophilic with the optimal salinity for growth being either 50 or 100, while two archaeal strains were extremely halophilic with an optimal growth salinity of 200. Additionally, we put forth strain SM.200-5 as a new candidate S alimicrobium species based on the phylogenic analysis of the 16 SrRNA gene sequence and its biochemical characteristics when compared with known related species.

Characterization of halophilic C_50 carotenoid-producing archaea isolated from solar saltworks in Bohai Bay,China

Halophilic archaea comprise the maj ority of microorganisms found in hypersaline environments.C50 carotenoids accumulated in archaea cells are considered potential biotechnological products and possess a number of biological functions.Ten red colonies were isolated from brine water in a saltern crystallizer pond of the Hangu Saltworks,China.16 S rRNA gene sequence analysis showed that the colonies belonged to the extremely halophilic archaea genera Halobacterium and Halorubrum.Two representative strains,Halobacterium strain SP-2 and Halorubrum strain SP-4,were selected for further study on the phenotypic characteristics and effects of salinity and pH on accumulation and composition of pigments in their cells.The archaeal strains were isolated and grown in a culture medium prepared by dissolving yeast extract(10 g/L) and acid-hydrolyzed casein(7.5 g/L) into brine water obtained from a local salt pond.Their optimum salinity and pH for growth were 250 and 7,respectively,although pigment accumulation(OD490/mL broth) was highest at pH 8.In addition,at 150-300 salinity,increasing salinity resulted in decreasing pigment accumulation.Analysis of the UV-Vis spectrum,TLC and HLPC chromatograms showed that C50 carotenoid bacterioruberin is the major pigment in both strains.

Complicated target recognition by archaeal box C/D guide RNAs

Box C/D RNAs guide the site-specific formation of 2′-O-methylated nucleotides(Nm)of RNAs in eukaryotes and archaea.Although C/D RNAs have been profiled in several archaea,their targets have not been experimentally determined.Here,we mapped Nm in r RNAs,t RNAs,and abundant small RNAs(s RNAs)and profiled C/D RNAs in the crenarchaeon Sulfolobus islandicus.The targets of C/D RNAs were assigned by analysis of base-pairing interactions,in vitro modification assays,and gene deletion experiments,revealing a complicated landscape of C/D RNA-target interactions.C/D RNAs widely use dual antisense elements to target adjacent sites in r RNAs,enhancing modification at weakly bound sites.Two consecutive sites can be guided with the same antisense element upstream of box D or D′,a phenomenon known as doublespecificity that is exclusive to internal box D′in eukaryotic C/D RNAs.Several C/D RNAs guide modification at a single non-canonical site.This study reveals the global landscape of RNA-guided 2′-O-methylation in an archaeon and unexpected targeting rules employed by C/D RNA.

The archaeal KEOPS complex possesses a functional Gon7 homolog and has an essential function independent of the cellular t^(6)A modification level

Kinase,putative Endopeptidase,and Other Proteins of Small size(KEOPS)is a multisubunit protein complex conserved in eukaryotes and archaea.It is composed of Pcc1,Kae1,Bud32,Cgi121,and Gon7 in eukaryotes and is primarily involved in N^(6)-threonylcarbamoyl adenosine(t^(6)A)modification of transfer RNAs(tRNAs).Recently,it was reported that KEOPS participates in homologous recombination(HR)repair in yeast.To characterize the KEOPS in archaea(aKEOPS),we conducted genetic and biochemical analyses of its encoding genes in the hyperthermophilic archaeon Saccharolobus islandicus.We show that aKEOPS also possesses five subunits,Pcc1,Kae1,Bud32,Cgi121,and Pcc1-like(or Gon7-like),just like eukaryotic KEOPS.Pcc1-like has physical interactions with Kae1 and Pcc1 and can mediate the monomerization of the dimeric subcomplex(Kae1-Pcc1-Pcc1-Kae1),suggesting that Pcc1-like is a functional homolog of the eukaryotic Gon7 subunit.Strikingly,none of the genes encoding aKEOPS subunits,including Pcc1 and Pcc1-like,can be deleted in the wild type and in a t^(6)A modification complementary strain named TsaKI,implying that the aKEOPS complex is essential for an additional cellular process in this archaeon.Knock-down of the Cgi121 subunit leads to severe growth retardance in the wild type that is partially rescued in TsaKI.These results suggest that aKEOPS plays an essential role independent of the cellular t^(6)A modification level.In addition,archaeal Cgi121 possesses dsDNA-binding activity that relies on its tRNA 3ʹCCA tail binding module.Our study clarifies the subunit organization of archaeal KEOPS and suggests an origin of eukaryotic Gon7.The study also reveals a possible link between the function in t^(6)A modification and the additional function,presumably HR.

纳米Fe_(3)O_(4)在煤微生物降解产CH_(4)过程中的催化作用

目的为了研究纳米Fe_(3)O_(4)在微生物降解煤产甲烷(CH_(4))过程中的催化作用,方法采用晋城矿区矿井水和中原油田土壤中的两种菌群(厌氧消化菌,义马矿区)的煤样,考查温度和纳米Fe_(3)O_(4)添加量对反应体系产CH_(4)摩尔浓度的影响,分析产CH_(4)过程中伴随气体CO_(2)和H_(2)的摩尔浓度变化及其对CH_(4)摩尔浓度的影响,评估厌氧消化产CH_(4)反应体系中铁的作用和最大负载量。结果通过分析厌氧性产CH_(4)古菌和多环芳烃分解菌共营降解煤的生物化学过程,认为煤降解产CH_(4)厌氧反应由两个主要步骤组成:一是稠环芳烃活化的羧化反应,该反应使煤被多环芳烃分解菌降解为甲苯酚和2-萘甲酸等化合物;二是产甲烷古菌利用煤分解产生的有机酸、甲基和气体等,通过辅酶的生物化学反应生成CH_(4),该过程CH_(4)产气量随温度升高而增大,起始反应需要大量CO_(2)气体。在产甲烷古菌和多环芳烃分解菌共营系统中添加纳米Fe_(3)O_(4)后,产CH_(4)量增加了39.6%~50.8%。纳米Fe_(3)O_(4)对生物化学过程的催化作用表现在促进中间产物(H_(2)和CO_(2)等)的生成,同时生物化学反应通过消耗H_(2)和含氧有机物并生成液态水以降低密闭实验系统的气体总压力,使催化反应持续正向进行。结论纳米Fe_(3)O_(4)对微生物降解煤产CH_(4)的催化作用需要多菌种互营环境,催化过程中存在最佳负载量。

New approaches for archaeal genome-guided cultivation

Archaea,one of the three domains of life along with Bacteria and Eukarya,contains ancient life forms such as methanogen that are observed today on Earth,and one lineage Asgard archaea is also considered the closest ancestor of Eukarya.Recently,with the development of interdisciplinary studies from Earth and Life sciences,archaeal organisms are considered to play pivotal roles in geochemical cycling in nature.However,our understanding of the attributes,origin and evolution,geochemical and ecological functions of Archaea is hampered by the scarcity of archaeal isolates,which has represented a challenge to researchers for the last 40 years.Cultivation-independent sequencing and phylogenomic analyses have demonstrated a considerable diversity of Archaea with more than 20 novel phyla.However,only four archaeal phyla have cultured representatives,leaving large gaps in our knowledge of the metabolic capabilities and ecological functions of the majority of archaeal strains identified exclusively by DNA sequencing.In this review,we summarize the discovery and development of archaeal research,highlight the knowledge gap between uncultured and cultured archaeal microbes,and call on the importance of devoting greater research efforts to archaeal cultivation.Finally,we outlined new ideas and strategic approaches,namely,(1)genome-based methods,(2)microbial network information-based methods,(3)genome-scale model-guided methods,and(4)machine learning methods,to enable the cultivation of uncultivated archaeal microbes using accumulated high-throughput sequencing data.

Community structure and activity potentials of archaeal communities in hadal sediments of the Mariana and Mussau trenches

Hadal trenches are the least explored marine habitat on earth. Archaea has been shown to be the dominant group in trench sediments. However, the activity potentials and detailed diversity of these communities as well as their inter-trench variations are still not known. In this study, we combined datasets from two pairs of primers to investigate at high resolution the structure and activity potentials of the archaeal communities in vertically sectioned sediment cores taken from the deepest points of the Mariana (10,853 m) and Mussau (7011 m) trenches. The compositions of the potentially active communities revealed, via 16S ribosomal RNA gene (rDNA) and RNA (rRNA), significant differences between samples. Marine Group I (MGI), with nine identified subgroups, was the most dominant class in the active archaeal communities of the two trenches. Significantly different species composition and vertical variations were observed between the two trenches. Vertical transitions from aerobic MGI α to anaerobic MGI η and υ subgroups were observed in MST but not in MT sediments, which might be related to the faster microbial oxygen consumption in MST. These results provide a better understanding on archaeal activity and diversity in trench sediments.

水稻品种间作对甲烷排放的影响

作物品种多样化种植是提高农业生态系统功能的有效措施,但不同品种混合种植能否影响温室气体排放仍然缺乏研究。本研究以水稻为例,通过原位盆栽试验,研究品种间隔种植(间作)对甲烷排放的影响。以甲烷高排放品种常农粳8号、皖稻153以及甲烷低排放品种苏香粳100、Ⅱ优084为供试材料,设置8个处理,包括4个水稻品种单一种植(单作),即常农粳8号单作(记作CN)、皖稻153单作(WD)、苏香粳100单作(SX)、Ⅱ优084单作(ⅡY),以及2个甲烷高排放品种与2个甲烷低排放品种间作,即常农粳8号+Ⅱ优084间作(CN+ⅡY)、常农粳8号+苏香粳100间作(CN+SX)、皖稻153+Ⅱ优084间作(WD+ⅡY)、皖稻153+苏香粳100间作(WD+SX)。间作品种按1∶1的株数比例间隔种植。结果表明,4个间作处理均能显著增加或维持水稻产量。不同间作处理的甲烷排放通量存在显著差异,与期望值相比,CN+SX处理显著降低甲烷的排放,而CN+ⅡY、WD+ⅡY处理则显著增加甲烷排放。与甲烷高排放品种的单作处理相比,苏香粳100与2个甲烷高排放品种间作时均能显著降低生长季土壤产甲烷古菌mcrA基因平均丰度,但Ⅱ优084仅在与皖稻153间作时有显著作用。除CN+SX外,其余3个间作处理下生长季土壤甲烷氧化菌pmoA基因平均丰度均显著低于所对应的单作处理。本研究认为可以通过水稻品种间作在获得增产的同时降低甲烷排放,但品种间作组合需要仔细筛选。