In this study, quantitative PCR (qPCR) and high-throughput sequencing were used to simultaneously examine both bacteria and fungi across temporal and spatial scales in activated sludge from ...wastewater treatment plants (WWTPs). The ratio of fungi to bacteria was 0.43% on average after accounting for the multicopies in 16S rRNA gene (54.63%), indicating the number of fungi was far lower than bacteria in active sludge. The Miseq sequencing results revealed obvious seasonal and spatial variations in bacterial and fungal distribution patterns in WWTPs. Compared to bacteria, fungi showed a lower divergence in alpha and beta diversity, and exhibited less taxonomic diversity in both abundant and rare subcommunities at the class level, suggesting that the fungal community was less variable in this artificial ecosystem. Such variation of microbial communities was significantly correlated with geographical distance, DO, temperature, HRT, SRT, COD, TN and TP. In activated sludge, the main function of bacteria was chemoheterotrophy, fermentation, and nitrogen cycling processes, while the dominant functional guilds of fungi were saprotroph, animal pathogen, and animal endosymbiont. Moreover, both bacteria and fungi could play important roles in the degradation of toxicants, like hydrocarbon and aromatic compounds.
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•In activated sludge samples, fungal to bacteria ratio was less than 1%.•Seasonal and spatial variations were observed in bacterial and fungal communities.•Fungi exhibited lower divergence in taxonomy, alpha and beta diversities than bacteria.•Bacteria and fungi owned different functions but worked jointly in activated sludge.
Microbial beta diversity has been recently studied along the water depth in aquatic ecosystems, however its turnover and nestedness components remain elusive especially for multiple taxonomic groups. ...Based on the beta diversity partitioning developed by Baselga and Local Contributions to Beta Diversity (LCBD) partitioning by Legendre, we examined the water-depth variations in beta diversity components of bacteria, archaea and fungi in surface sediments of Hulun Lake, a semi-arid lake in northern China, and further explored the relative importance of environmental drivers underlying their patterns. We found that the relative abundances of
Proteobacteria
,
Chloroflexi
,
Euryarchaeota
, and
Rozellomycota
increased toward deep water, while
Acidobacteria
,
Parvarchaeota
, and
Chytridiomycota
decreased. For bacteria and archaea, there were significant (
p
< 0.05) decreasing water-depth patterns for LCBD and LCBD
Repl
(i.e., species replacement), while increasing patterns for total beta diversity and turnover, implying that total beta diversity and LCBD were dominated by species turnover or LCBD
Repl
. Further, bacteria showed a strong correlation with archaea regarding LCBD, total beta diversity and turnover. Such parallel patterns among bacteria and archaea were underpinned by similar ecological processes like environmental selection. Total beta diversity and turnover were largely affected by sediment total nitrogen, while LCBD and LCBD
Repl
were mainly constrained by water NO
2
−
-N and NO
3
−
-N. For fungal community variation, no significant patterns were observed, which may be due to different drivers like water nitrogen or phosphorus. Taken together, our findings provide compelling evidences for disentangling the underlying mechanisms of community variation in multiple aquatic microbial taxonomic groups.
Today, cloud storage becomes one of the critical services, because users can easily modify and share data with others in cloud. However, the integrity of shared cloud data is vulnerable to inevitable ...hardware faults, software failures or human errors. To ensure the integrity of the shared data, some schemes have been designed to allow public verifiers (i.e., third party auditors) to efficiently audit data integrity without retrieving the entire users' data from cloud. Unfortunately, public auditing on the integrity of shared data may reveal data owners' sensitive information to the third party auditor. In this paper, we propose a new privacy-aware public auditing mechanism for shared cloud data by constructing a homomorphic verifiable group signature. Unlike the existing solutions, our scheme requires at least t group managers to recover a trace key cooperatively, which eliminates the abuse of single-authority power and provides non-frameability. Moreover, our scheme ensures that group users can trace data changes through designated binary tree; and can recover the latest correct data block when the current data block is damaged. In addition, the formal security analysis and experimental results indicate that our scheme is provably secure and efficient.
The investigation of chemical speciation of primary toxic metal(loid)s (Cd, Pb, and As) in soil profile in nonferrous metal smelting site is a key to the assessment of their mobility characteristics ...and formulation of subsequent remediation strategy. In this study, 74 soil samples were collected at 12 different soil profiles; soil physio-chemical properties and total content of Cd, Pb and As and corresponding chemical speciation were also determined. The results showed that the mean total concentration followed the order of Pb > As > Cd. A large proportion of Pb, Cd and As were accumulated in upper soil profiles (depth < 3 m). Heavy pollution of Pb, Cd and As were observed in the whole soil profile at the area of fuel oil storage tank (ZY6) and lead smelting area (ZY8). The dominant fraction of Cd was exchangeable fraction (F1); Pb was dominant in Fe/Mn oxides-bound fraction (F3) in most cases; Crystallized Fe/Al hydrous oxides bound fraction (F4) generally accounted for a large proportion of As. Mobility factor (MF) followed the order Cd > As > Pb, indicating that Cd was the most mobile element in soil profiles. Pearson correlation analysis found that MFCd was significantly positively correlated to soil silt; the F4 fraction percentage of As was significantly positively correlated to soil redox potential (Eh). Additionally, MFCd/Pb was found to be positively correlated to crystalline iron (Fec), while negatively correlated to amorphous iron (Feo). The findings reported in this study, on the basis of distribution characteristics of chemical speciation could provide a new solution for future soil remediation at the site. Long-term solutions to metal(loid)s pollution might be offered by microbial-assisted soil washing technique that promotes the transformation of Fe/Mn oxides-bound fraction and organic/sulfide-bound fraction.
•The mean accumulation amount followed the order of Pb > As > Cd.•Toxic metal(loid)s mainly occurred at soil profiles in the depth < 3 m.•Cd was dominant in exchangeable fraction showing highest mobility in soil profiles.
Understanding the abundance change of certain bacterial taxa is quite important for the study of soil microbiology. However, the observed differences of relative abundances by high-throughput ...techniques may not accurately reflect those of the actual taxon abundances. This study investigated whether soil microbial abundances coupling with microbial quantities can be more informative in describing the microbial population distribution under different locations. We analyzed relative abundances of the major species in soil microbial communities from Beijing and Tibet grasslands by using 16 S rRNA high-throughput sequencing technique, and quantified the absolute bacterial cell numbers directly or indirectly by multiple culture-independent measurements, including adenosine tri-phosphate (ATP), flow cytometry (FCM), quantitative real-time PCR (qPCR), phospholipid fatty acids (PLFA) and microbial biomass Carbon (MBC). By comparison of the relative abundance and the estimated absolute abundances (EAA) of the major components in soil microbial communities, several dominant phyla, including Actinobacteria, Bacteroidetes, Verrucomicrobia, Chloroflexi, Gemmatimonates and Planctomycetes, showed significantly different trends. These results indicated that the change in EAA might be more informative in describing the dynamics of a population in a community. Further studies of soil microbes should combine the quantification and relative abundances of the microbial communities for the comparisons among various locations.
Microorganisms that exhibit resistance to environmental stressors, particularly heavy metals, have the potential to be used in bioremediation strategies. This study aimed to explore and identify ...microorganisms that are resistant to heavy metals in soil environments as potential candidates for bioremediation. Metagenomic analysis was conducted using microbiome metagenomes obtained from the rhizosphere of soil contaminated with heavy metals and mineral-affected soil. The analysis resulted in the recovery of a total of 175 metagenome-assembled genomes (MAGs), 73 of which were potentially representing novel taxonomic levels beyond the genus level. The constructed ecological network revealed the presence of keystone taxa, including
, and
. Among the recovered MAGs, 50 were associated with these keystone taxa. Notably, these MAGs displayed an abundance of genes conferring resistance to heavy metals and other abiotic stresses, particularly those affiliated with the keystone taxa. These genes were found to combat excessive accumulation of zinc/manganese, arsenate/arsenite, chromate, nickel/cobalt, copper, and tellurite. Furthermore, the keystone taxa were found to utilize both organic and inorganic energy sources, such as sulfur, arsenic, and carbon dioxide. Additionally, these keystone taxa exhibited the ability to promote vegetation development in re-vegetated mining areas through phosphorus solubilization and metabolite secretion. In summary, our study highlights the metabolic adaptability and ecological significance of microbial keystone taxa in mineral-affected soils. The MAGs associated with keystone taxa exhibited a markedly higher number of genes related to abiotic stress resistance and plant growth promotion compared to non-keystone taxa MAGs.
Members of the genus
, which can adapt to extremely high concentrations of heavy metals, are universally found at acid mine drainage (AMD) sites. Here, we performed a comparative genomic analysis of ...37 strains within the genus
to answer the untouched questions as to the mechanisms and the evolutionary history of metal resistance genes in
spp. The results showed that the evolutionary history of metal resistance genes in
spp. involved a combination of gene gains and losses, horizontal gene transfer (HGT), and gene duplication. Phylogenetic analyses revealed that metal resistance genes in
spp. were acquired by early HGT events from species that shared habitats with
spp., such as
,
,
, and
species. Multicopper oxidase genes involved in copper detoxification were lost in iron-oxidizing
,
, and
and were replaced by rusticyanin genes during evolution. In addition, widespread purifying selection and the predicted high expression levels emphasized the indispensable roles of metal resistance genes in the ability of
spp. to adapt to harsh environments. Altogether, the results suggested that
spp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. This study sheds light on the distribution, organization, functionality, and complex evolutionary history of metal resistance genes in
spp.
Horizontal gene transfer (HGT), natural selection, and gene duplication are three main engines that drive the adaptive evolution of microbial genomes. Previous studies indicated that HGT was a main adaptive mechanism in acidophiles to cope with heavy-metal-rich environments. However, evidences of HGT in
species in response to challenging metal-rich environments and the mechanisms addressing how metal resistance genes originated and evolved in
are still lacking. The findings of this study revealed a fascinating phenomenon of putative cross-phylum HGT, suggesting that
spp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. Altogether, the insights gained in this study have improved our understanding of the metal resistance strategies of
spp.
An updated sul1 gene sequence database was constructed and new degenerate primers were designed to better investigate the abundance, diversity, and variation of a ubiquitous antibiotic resistance ...gene, sul1, with PCR-based methods in activated sludge from wastewater treatment plants (WWTPs). The newly designed degenerate primers showed high specificity and higher coverage in both in-silico evaluations and activated sludge samples compared to previous sul1 primers. Using the new primers, the abundance and diversity of sul1 gene, together with 16S rRNA gene, in activated sludge from five WWTPs in summer and winter were determined by quantitative PCR and MiSeq sequencing. The sul1 gene was found to be prevalent and displayed a comparable abundance (0.081 copies per bacterial cell in average) to the total bacteria across all samples. However, compared to the significant seasonal and geographical divergences in the quantity and diversity of bacterial communities in WWTPs, there were no significant seasonal or geographical variations of representative clusters of sul1 gene in most cases. Additionally, the representative sul1 clusters showed fairly close phylogeny and there was no obvious correlation between sul1 gene and the dominant bacterial genera, as well as the int1 gene, suggesting that bacterial hosts of sul1 gene is not stable, the sul1 gene may be carried by mobile genetic elements, sometimes integrated with class 1 integrons and sometimes not. Thus mobile genetic elements likely play a greater role than specific microbial taxa in determining the composition of sul1 gene in WWTPs.
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•The newly designed degenerate primers of sul1 gene exhibited high efficiency.•In activated sludge samples, sul1 gene was prevalent with high abundance.•The distribution and phylogeny of sul1 gene is highly similar across all samples.•Mobile genetic elements mostly shift the composition of sul1 gene in WWTPs.
Metagenomics allows us to acquire the potential resources from both cultivatable and uncultivable microorganisms in the environment. Here, shotgun metagenome sequencing was used to investigate ...microbial communities from the surface layer of low grade copper tailings that were industrially bioleached at the Dexing Copper Mine, China. A bioinformatics analysis was further performed to elucidate structural and functional properties of the microbial communities in a copper bioleaching heap.
Taxonomic analysis revealed unexpectedly high microbial biodiversity of this extremely acidic environment, as most sequences were phylogenetically assigned to Proteobacteria, while Euryarchaeota-related sequences occupied little proportion in this system, assuming that Archaea probably played little role in the bioleaching systems. At the genus level, the microbial community in mineral surface-layer was dominated by the sulfur- and iron-oxidizing acidophiles such as Acidithiobacillus-like populations, most of which were A. ferrivorans-like and A. ferrooxidans-like groups. In addition, Caudovirales were the dominant viral type observed in this extremely environment. Functional analysis illustrated that the principal participants related to the key metabolic pathways (carbon fixation, nitrogen metabolism, Fe(II) oxidation and sulfur metabolism) were mainly identified to be Acidithiobacillus-like, Thiobacillus-like and Leptospirillum-like microorganisms, indicating their vital roles. Also, microbial community harbored certain adaptive mechanisms (heavy metal resistance, low pH adaption, organic solvents tolerance and detoxification of hydroxyl radicals) as they performed their functions in the bioleaching system.
Our study provides several valuable datasets for understanding the microbial community composition and function in the surface-layer of copper bioleaching heap.
•Significant cross-taxon congruence was found among bacteria, fungi, and zoobenthos.•Fungal community was more resistant to eutrophication compared to bacteria and zoobenthos.•Eutrophication ...decreased cross-taxon congruence in sediment biodiversity.•Bacteria worked as stabilizer in sediment ecosystem.
Eutrophication is a major problem currently affecting sediment biodiversity in different kingdoms. Surveys at different spatial scales have suggested that nutrient enrichment drove the congruence in biodiversity across different kingdoms. In this study, we examined the diversity indexes of bacteria, fungi, and zoobenthos in Dongting Lake, which is undergoing different trophic levels. The species richness and Shannon index of bacteria, fungi, and zoobenthos were all consistent with the intermediate disturbance hypothesis along the content of TN and TP, with the hysteresis of fungal group. Significant cross-taxon congruence was found in species richness between bacteria and zoobenthos, and Shannon index between bacteria and fungi. Also, the strength of congruence in biodiversity among bacteria, fungi and zoobenthos would decrease along nutrient enrichment. Multi- and single-kingdom networks found that bacterial group contained more nodes and edges compared to fungal and zoobenthos groups, and bacterial removal led to the lowest natural connectivity. And highest positive interaction proportion and lowest absolute value of natural connectivity slope were observed in zoobenthos group. These results highlighted the importance of bacteria as stabilizer in sediment ecosystem, and the most sensitive feature of zoobenthos to nutrient enrichment. Taken together, our results confirmed the cross-taxon congruence between multi-kingdoms, and the effectiveness of bacteria as a potential bioindicator of ecological change.
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