Paleomicrobiology to investigate copper resistance in bacteria: isolation and description ofCupriavidus necatorB9 in the soil of a medieval foundry

Insight into the microbial diversity and community in the sacrificial pits of Sanxingdui site (Sichuan, China)

Introduction

The Sanxingdui site (Sichuan, China) is the typical representative of the ancient Shu culture, which lasts from the late Neolithic to early Western Zhou. The sacrificial pits are located in the core region of Sanxingdui site, and numerous artifacts are unearthed including ivory, seashells, bronzes, pottery, jade, stone, gold, bone, and horn products. The function of the pits and buried artifacts has always been the focus, but the microbiome around artifacts attracts less attention. Recently, the microbiome in buried ivory soil has just been identified; however, the microbiome around other artifacts has never been studied. In term of the unique perspective for interpretation the archaeological issues, the study was carried out for: (1) the microbial diversity and community of soil in the lower layer of artifacts in sacrificial pits, (2) the potential biodeterioration behavior of organic and inorganic relics, and (3) the impact of sacrificial and burial activities in different sacrificial pits on microbiome.

Methods

There were 45 soil samples around different artifacts in three sacrificial pits and 12 raw soil samples inside or outside the sacrificial pit sampling from Sanxingdui site. The microbial genomes were then identified and analyzed using the next-generation high-throughput sequencing.

Results

The represented bacterial phyla were Proteobacteria, Actinobacteriota, GAL15, Chloroflexi, Acidobacteriota, Methylomirabilota, Thermoplasmatota, Crenarchaeota, Gemmatimonadota, and Firmicutes, and the represented fungal phyla were Ascomycota, Mortierellomycota, and Basidiomycota. Further microbial functional analysis found that the bacterial genera Sphingopyxis, Limnobacter, and Streptomyces and the fungal genera Cladosporium, Acremonium, and Mortierella were concerned with the degradation of organic matter, while the genera Pseudomonas, Arthrobacter, Variovorax, Aspergillus, and Penicillium might be related to the biocorrosion of bronzes. In addition, the microbial composition and principal co-ordinate analysis (PCoA) demonstrated the significant differences in microbial composition and structure between the raw soil samples and the soil samples around the artifacts and also between the soil samples in different sacrificial pits.

Discussion

It is important to understand the biodeterioration of the buried artifacts and the sacrificial activities in Sanxingdui site according to the results of microbial diversity and community. The combination of microbiology and archaeology will shed light on the archaeological issues related to the ancient human activities and behaviors.

Cupriavidus in the intestinal microbiota of Tibet endemic fish Glyptosternum maculatum can help it adapt to habitat of the Qinghai Tibet Plateau

Background

Gut microbes play an important role in the growth and development of fish. The Tibetan Plateau fish Glyptosternum maculatum is a unique species of sisorid catfish living in the river up to 4200 m altitude.

Results

To understand the mechanisms underlying the ability of G. maculatum to adapt to the high-altitude habitat, the intestinal microbiota of G. maculatum was studied. We used high-throughput sequencing of the 16S ribosomal RNA gene of intestinal microorganisms of wild and cultured G. maculatum to explore the characteristics of intestinal microorganisms and compared the gut microbial community of wild and cultured G. maculatum. The results showed that the α-diversity and richness of the intestinal microbiome were higher in wild G. maculatum than in cultured fish. The most abundant phylum in both G. maculatum were Fusobacteria, Proteobacteria, Firmicutes, and Bacteroidetes; Cetobacterium and Cupriavidus are the most dominant genus. The membership and structure of intestinal bacterial communities in wild G. maculatum are similar to the cultured fish, suggesting that a core microbiota is present in both G. maculatum intestinal bacterial communities. Metastats analysis showed that six genera were differentially represented between the wild and cultured G. maculatum.

Conclusions

The most interesting characteristic of the intestinal microbial communities of G. maculatum is that there were large numbers of Cupriavidus, which may play an important role in the adaptation of G. maculatum to the water of the Yarlung Zangbo River with a high Cu content. This result, in turn, can guide us on breeding G. maculatum.

Optimizing Bioremediation: Elucidating Copper Accumulation Mechanisms of Acinetobacter sp. IrC2 Isolated From an Industrial Waste Treatment Center

Acinetobacter sp. IrC2 is a copper-resistant bacterium isolated from an industrial waste treatment center in Rungkut, Surabaya. Copper-resistant bacteria are known to accumulate copper inside the cells as a mechanism to adapt to a copper-contaminated environment. Periplasmic and membrane proteins CopA and CopB have been known to incorporate copper as a mechanism of copper resistance. In the present study, protein profile changes in Acinetobacter sp. IrC2 following exposure to copper stress were analyzed to elucidate the copper resistance mechanism. Bacteria were grown in a Luria Bertani agar medium with and without CuSO4 supplementation. Intracellular copper ion accumulation was quantified using atomic absorption spectrophotometry. Changes in protein profile were assessed using sodium dodecyl sulfate polyacrylamide gel electrophoresis. The results showed that 6 mM CuSO4 was toxic for Acinetobacter sp. IrC2, and as a response to this copper-stress condition, the lag phase was prolonged to 18 h. It was also found that the bacteria accumulated copper to a level of 508.01 mg/g of cells' dry weight, marked by a change in colony color to green. The protein profile under copper stress was altered as evidenced by the appearance of five specific protein bands with molecular weights of 68.0, 60.5, 38.5, 24.0, and 20.5 kDa, suggesting the presence of CopA, multicopper oxidase (MCO), CopB, universal stress protein (Usp), and superoxide dismutase (SOD) and/or DNA-binding protein from starved cells, respectively. We proposed that the mechanism of bacterial resistance to copper involves CopA and CopB membrane proteins in binding Cu ions in the periplasm and excreting excess Cu ions as well as involving enzymes that play a role in the detoxification process, namely, SOD, MCO, and Usp to avoid cell damage under copper stress.

Synthetic biology approaches to copper remediation: bioleaching, accumulation and recycling

One of the current aims of synthetic biology is the development of novel microorganisms that can mine economically important elements from the environment or remediate toxic waste compounds. Copper, in particular, is a high-priority target for bioremediation owing to its extensive use in the food, metal and electronic industries and its resulting common presence as an environmental pollutant. Even though microbe-aided copper biomining is a mature technology, its application to waste treatment and remediation of contaminated sites still requires further research and development. Crucially, any engineered copper-remediating chassis must survive in copper-rich environments and adapt to copper toxicity; they also require bespoke adaptations to specifically extract copper and safely accumulate it as a human-recoverable deposit to enable biorecycling. Here, we review current strategies in copper bioremediation, biomining and biorecycling, as well as strategies that extant bacteria use to enhance copper tolerance, accumulation and mineralization in the native environment. By describing the existing toolbox of copper homeostasis proteins from naturally occurring bacteria, we show how these modular systems can be exploited through synthetic biology to enhance the properties of engineered microbes for biotechnological copper recovery applications.

Adaptation of Cupriavidus metallidurans CH34 to Toxic Zinc Concentrations Involves an Uncharacterized ABC-Type Transporter

Cupriavidus metallidurans CH34 is a well-studied metal-resistant β-proteobacterium and contains a battery of genes participating in metal metabolism and resistance. Here, we generated a mutant (CH34^ZnR) adapted to high zinc concentrations in order to study how CH34 could adaptively further increase its resistance against this metal. Characterization of CH34^ZnR revealed that it was also more resistant to cadmium, and that it incurred seven insertion sequence-mediated mutations. Among these, an IS1088 disruption of the glpR gene (encoding a DeoR-type transcriptional repressor) resulted in the constitutive expression of the neighboring ATP-binding cassette (ABC)-type transporter. GlpR and the adjacent ABC transporter are highly similar to the glycerol operon regulator and ATP-driven glycerol importer of Rhizobium leguminosarum bv. viciae VF39, respectively. Deletion of glpR or the ABC transporter and complementation of CH34^ZnR with the parental glpR gene further demonstrated that loss of GlpR function and concomitant derepression of the adjacent ABC transporter is pivotal for the observed resistance phenotype. Importantly, addition of glycerol, presumably by glycerol-mediated attenuation of GlpR activity, also promoted increased zinc and cadmium resistance in the parental CH34 strain. Upregulation of this ABC-type transporter is therefore proposed as a new adaptation route towards metal resistance.

Dynamic proteome responses to sequential reduction of Cr(VI) and adsorption of Pb(II) by Pannonibacter phragmitetus BB

Here, the microbial responses to Cr(VI) and Pb(II) with bio-removal of the metals in water by Pannonibacter phragmitetus BB were explored. The comparative bacterial proteomics showed that the intracellular and extracellular Cr(VI) reduction proteins, Pb(II) adsorption by the lipoprotein and sugar-related bacterial proteins, as well as Pb(II) precipitation by phosphate and OH^- were vital to the bio-removal of Cr(VI) and Pb(II). Moreover, the influx and efflux channels of Cr(VI) and Cr(III), Pb(II) transporters, extracellular siderophores for Pb(II) complexation and antioxidant proteins enabled the strain BB to resist the toxicity of Cr(VI) and Pb(II). In addition, the dynamic expression levels of the proteins related to reduction and transportation of Cr(VI), and adsorption, transportation and complexation of Pb(II) were dependent on the corresponding metal, respectively. The anti-oxidative stress system, such as superoxide dismutase, and Na⁺/H⁺ antiporters played central roles in the protein-protein interaction network to resist and detoxify Cr(VI) and Pb(II). The results of our study provide a novel insight for the physiological responses of the strain BB to the combined stresses of Pb(II) and Cr(VI).

Impact of copper on the diazotroph abundance and community composition during swine manure composting

Biological nitrogen fixation is a major pathway in ecosystems. This study investigated the effects of adding Cu at different levels (0, 200, and 2000 mg kg^-1) on the diazotroph community during swine manure composting. Quantitative PCR and high-throughput sequencing were used to analyze the abundances of diazotrophs and the community composition based on the nifH gene. The nifH gene copy number was relatively high in the early stage of composting and Cu had a significant inhibitory effect on the nifH copy number. Furthermore, Cu decreased the diversity of nifH and changed the microbial community structure in the early stage. The nifH genes from members of Firmicutes and Clostridium were most abundant. Co-occurrence ecological network analysis showed that the Cu treatments affected the co-occurrence patterns of diazotroph communities and reduced the associations between different diazotrophs. Interestingly, Cu may weaken symbiotic diazotrophic interactions and enhance the roles of free-living diazotrophs.

The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial

Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis, Methylophilus methylotrophus, Nitrosospira, and Lysobacter mobilis. The capacity to track alterations of an amplified microbial community at high taxonomic resolution using modern bioinformatic approaches, as well as identifying where that resolution is lost for technical or biological reasons, provides an insight into the complexity of the microbial world resisting anthropogenic pollution. While functional assessment of uncharacterized organisms within environmental samples is technically challenging, an important step is observing those organisms able to tolerate extreme stress and to recognize the extent to which important amplifiable community members still require characterization.