Analysis and interpretation of hot springs water, biofilms, and sediment bacterial community profiling and their metabolic potential in the area of Taiwan geothermal ecosystem

Spatial scale modulates stochastic and deterministic influence on biogeography of photosynthetic biofilms in Southeast Asian hot springs

Hot springs, with their well-characterized major abiotic variables and island-like habitats, are ideal systems for studying microbial biogeography. Photosynthetic biofilms are a major biological feature of hot springs but despite this large-scale studies are scarce, leaving critical questions about the drivers of spatial turnover unanswered. Here, we analysed 395 photosynthetic biofilms from neutral-alkaline hot springs (39-66 °C, pH 6.4-9.0) across a 2100 km latitudinal gradient in Southeast Asia. The Cyanobacteria-dominated communities were categorized into six biogeographic regions, each characterized by a distinct core microbiome and biotic interactions. We observed a significant decline in the explanatory power of major abiotic variables with increasing spatial scale, from 62.6% locally, 55% regionally, to 26.8% for the inter-regional meta-community. Statistical null models revealed that deterministic environmental filtering predominated at local and regional scales, whereas stochastic ecological drift was more influential at the inter-regional scale. These findings enhance our understanding of the differential contribution of ecological drivers and highlight the importance of spatial scale in shaping biogeographic distributions for microorganisms.

Deciphering the distribution and enrichment of arsenic in geothermal water in the Red River Fault Zone, southwest China

High-arsenic (As) geothermal water has been found over the world. However, the spatial distributions of As contents and genesis in geothermal systems remain to be fully understood due to the complexity of the sources and processes associated with As. In this study, the hydrochemical and isotopic methods and the self-organized mapping (SOM) were employed to investigate the spatial distributions and enrichment mechanism of As in hot springs in the Red River Fault Zone, southwest China. The results showed that arsenic concentration is low (less than 10 µg/L) in hot springs in the south part of the fault, while it is relatively high with a mean value of 212.73 µg/L in the north part of the fault. The distinct spatial differences in arsenic concentration of hot springs may be attributed to the heterogeneity of lithologies along the fault zone, with sedimentary rocks dominated in the northern and metamorphic rocks dominated in the southern section of the fault. Two sources of arsenic can be identified in the study area: 1) As is correlated with typical geothermal species such as Li and B, indicating that rock leaching from deep geothermal reservoirs can be a dominant source of As; 2) high level of HCO3- and weak alkalinity condition caused the desorption of arsenic from the sediment surface. In addition, the mixing with shallow groundwater also affects the As contents in hot springs. This study provides an insight into the formation and controls on high-arsenic geothermal water.

Root-associated functional microbiome endemism facilitates heavy metal resilience and nutrient poor adaptation in native plants under serpentine driven edaphic challenges

Serpentine soils are characterized by high concentrations of heavy metals (HMs) and limited essential nutrients with remarkable endemic plant diversity, yet the mechanisms enabling plant adaptation to thrive in such harsh environments remain largely unknown. Full-length 16S rRNA amplicon sequencing, coupled with physiological and functional assays, was used to explore root-associated bacterial community composition and their metabolic and ecological functions. The results revealed that serpentine plant species exhibited significantly higher metal transfer factor values compared to non-serpentine plant species, particularly evident in Bidens pilosa, Miscanthus floridulus, and Leucaena leucocephala. The serpentine root-associated microbes showed a higher utilization of carboxylic acid, whereas carbohydrate utilization was higher in the non-serpentine site. Zymomonas mobilis and Flavabacterium sp. exhibited high resistance to heavy metal concentrations, showing greater adaptability, while, Staphylococcus carnosus showed sensitivity to HMs, showing limited adaptability. Moreover, Ni, Cr, and Co resistance genes were found, while nitrogen and phosphorous metabolism genes were less abundant in the serpentine site compared to the non-serpentine site. Furthermore, Flavobacterium sp. had a strong positive relationship with Cd and Cu, Zymomonas mobilis with Ni, and Cr, Streptomyces sp. with Co, and Staphylococcus carnosus with N and P cycling. These findings underscore critical role of root-associated bacterial communities and distinctive soil conditions of serpentine habitats in fostering ecological adaptation of native plant species to the challenges posed by HMs and nutrient deficiencies.

Global transcriptional analysis for molecular responses of Alicyclobacillus acidoterrestris spores in drinking water after low- and medium-pressure ultraviolet irradiation

Ultraviolet (UV) irradiation can effectively disinfect water contaminated with pathogens. However, the biological mechanisms of inactivation by different types of UV irradiation are unknown. The present study investigated the inactivation mechanisms of Alicyclobacillus acidoterrestris spores in water by low-pressure UV (LPUV) and medium-pressure UV (MPUV) using a quasi-collimated beam apparatus. Global transcriptomic data obtained by RNA-seq revealed 291 shared differentially expressed genes (DEGs) that damaged DNA, reduced biofilm formation, and had other reactions. The individual downregulated DEGs (n = 123) mainly related to cell motility, membrane transport, and metabolism were induced by LPUV, and in turn contributed to energy-saving and metabolic activity inhibition, forcing bacteria into a viable but non-culturable (VBNC) state. The individual upregulated DEGs (n = 244) following MPUV treatment were mainly enriched in cell motility, membrane transport, metabolism, DNA replication and repair, and spore germination pathways. This results in high-energy consumption, severe damage to genetic material, and enhanced spore germination accelerated cell death. Additionally, hub genes in the protein-protein interaction network were mainly involved in transcription and translation. These findings contribute to the comprehensive understanding of the inactivation mechanisms of different types of UV irradiation, and will improve applications of UV disinfection in the treatment of water.

S0-dependent bio-reduction for antimonate detoxification from wastewater by an autotrophic bioreactor with internal recirculation

Elemental sulfur (S0) autotrophic reduction is a promising approach for antimonate [Sb(V)] removal from water; however, it is hard to achieve effective removal of total antimony (TSb). This study established internal recirculation in an S0 autotrophic bioreactor (SABIR) to enhance TSb removal from Sb(V)-contaminated water. Complete Sb(V) reduction (10 mg/L) with bare residual Sb(III) (< 0.26 mg/L) was achieved at hydraulic retention time (HRT) = 8 h. Shortening HRT adversely affected the removal efficiencies of Sb(V) and TSb; meanwhile, an increased reflux ratio was conducive to Sb(V) and TSb removal at the same HRT. Sulfur disproportionation occurred in the SABIR and was the primary source for SO42- generation and alkalinity consumption. The alkalinity consumption decreased with the shortening HRT and increased with an increased reflux ratio at the same HRT. The generated SO42- was significantly higher (50-100 times) than the theoretical value for Sb(V) reduction. Coefficient of variation (CV), first-order kinetic models, and osmolality analyses showed that internal recirculation did not significantly affect the stability of SABIR but contributed to enhancing TSb removal by increasing mass transfer and reflowing generated sulfide back to the SABIR. SEM-EDS, Raman spectroscopy, XRD and XPS analyses identified that the precipitates in the SABIR were Sb2S3 and Sb-S compounds. In addition, high-throughput sequencing analysis revealed the microbial community structure's temporal and spatial distribution in the SABIR. Dominant genera, including unclassified-Proteobacteria (18.72-38.99%), Thiomonas (0.94-4.87%) and Desulfitobacterium (1.18-2.75%) might be responsible for Sb(V) bio-reduction and removal. This study provides a strategy to remove Sb from water effectively and supports the theoretical basis for the practical application of the SABIR in Sb(V)-contaminated wastewater.

Evaluating groundwater ecosystem dynamics in response to post in-situ remediation of mixed chlorinated volatile organic compounds (CVOCs): An insight into microbial community resilience, adaptability, and metabolic functionality for sustainable remediation and ecosystem restoration

The in-situ remediation of groundwater contaminated with mixed chlorinated volatile organic compounds (CVOCs) has become a significant global research interest. However, limited attention has been given in understanding the effects of these remediation efforts on the groundwater microbial communities, which are vital for maintaining ecosystem health through their involvement in biogeochemical cycles. Hence, this study aimed to provide valuable insights into the impacts of in-situ remediation methods on groundwater microbial communities and ecosystem functionality, employing high-throughput sequencing coupled with functional and physiological assays. The results showed that both bioremediation and chemical remediation methods adversely affected microbial diversity and abundance compared to non-polluted sites. Certain taxa such as Pseudomonas, Acinetobacter, and Vogesella were sensitive to these remediation methods, while Aquabacterium exhibited greater adaptability. Functional annotation unveiled the beneficial impact of bioremediation on the sulfur cycle and specific taxa such as Cellvibrio, Massilia, Algoriphagus, and Flavobacterium which showed a significant positive relationship with dark oxidation of sulfur compounds. In contrast, chemical remediation showed adverse impacts on the nitrogen cycle with a reduced abundance of nitrogen and nitrate respiration along with a reduced utilization of amines (nitrogen rich substrate). The findings of this study offer valuable insights into the potential impacts of in-situ remediation methods on groundwater microbial communities and ecosystem functionality, emphasizing the need for meticulous consideration to ensure the implementation of effective and sustainable remediation strategies that safeguard ecosystem health and function.

Unraveling the shift in bacterial communities profile grown in sediments co-contaminated with chlorolignin waste of pulp-paper mill by metagenomics approach

Pulp-paper mills (PPMs) are known for consistently generating a wide variety of pollutants, that are often unidentified and highly resistant to environmental degradation. The current study aims to investigate the changes in the indigenous bacterial communities profile grown in the sediment co-contaminated with organic and inorganic pollutants discharged from the PPMs. The two sediment samples, designated PPS-1 and PPS-2, were collected from two different sites. Physico-chemical characterization of PPS-1 and PPS-2 revealed the presence of heavy metals (mg kg-1) like Cu (0.009-0.01), Ni (0.005-0.002), Mn (0.078-0.056), Cr (0.015-0.009), Pb (0.008-0.006), Zn (0.225-0.086), Fe (2.124-0.764), Al (3.477-22.277), and Ti (99.792-45.012) along with high content of chlorophenol, and lignin. The comparative analysis of organic pollutants in sediment samples using gas chromatography-mass spectrometry (GC-MS) revealed the presence of major highly refractory compounds, such as stigmasterol, β-sitosterol, hexadecanoic acid, octadecanoic acid; 2,4-di-tert-butylphenol; heptacosane; dimethyl phthalate; hexachlorobenzene; 1-decanol,2-hexyl; furane 2,5-dimethyl, etc in sediment samples which are reported as a potential toxic compounds. Simultaneously, high-throughput sequencing targeting the V3-V4 hypervariable region of the 16S rRNA genes, resulted in the identification of 1,249 and 1,345 operational taxonomic units (OTUs) derived from a total of 115,665 and 119,386 sequences read, in PPS-1 and PPS-2, respectively. Analysis of rarefaction curves indicated a diversity in OTU abundance between PPS-1 (1,249 OTUs) and PPS-2 (1,345 OTUs). Furthermore, taxonomic assignment of metagenomics sequence data showed that Proteobacteria (55.40%; 56.30%), Bacteoidetes (11.30%; 12.20%), and Planctomycetes (5.40%; 4.70%) were the most abundant phyla; Alphproteobacteria (20.50%; 23.50%), Betaproteobacteria (16.00%; 12.30%), and Gammaproteobacteria were the most recorded classes in PPS-1 and PPS-2, respectively. At the genus level, Thiobacillus (7.60%; 4.50%) was the most abundant genera grown in sediment samples. The results indicate significant differences in both the diversity and relative abundance of taxa in the bacterial communities associated with PPS-2 when compared to PPS-1. This study unveils key insights into contaminant characteristics and shifts in bacterial communities within contaminated environments. It highlights the potential for developing efficient bioremediation techniques to restore ecological balance in pulp-paper mill waste-polluted areas, stressing the importance of identifying a significant percentage of unclassified genera and species to explore novel genes.

Bacterial community analysis identifies Klebsiella pneumoniae as a native symbiotic bacterium in the newborn Protobothrops mucrosquamatus

BACKGROUND

The study of the native microbiome of organisms is crucial. The connection between the native microbiome and the host affects the formation of the innate immune system and the organism's growth. However, the native microbiome of newborn venomous snakes has not been reported. Therefore, we aimed to determine the oral and skin microbiomes of newborn Protobothrops mucrosquamatus.

RESULTS

We performed 16 S full-length sequencing on 14 samples collected from 7 newborn P. mucrosquamatus individuals, specifically targeting their oral and skin microbiomes. In terms of the oral and skin microbiome, the main species were Klebsiella pneumoniae lineages. According to subspecies/species analysis, the proportion from highest to lowest was K. quasipneumoniae subsp. similipneumoniae, K. pneumoniae subsp. pneumoniae, and K. pneumoniae subsp. rhinoscleromatis. These three bacteria accounted for 62.5% and 85% of the skin and oral activity, respectively. The oral microbiome of newborn P. mucrosquamatus did not comprise common bacteria found in snakebite wounds or oral cultures in adult snakes. Therefore, the source of other microbiomes in the oral cavities of adult snakes may be the environment or prey. Functional Annotation of the Prokaryotic Taxa analysis showed that the skin/oral native microbiome metabolism was related to fermentation and human infection owing to the dominance of K. pneumoniae lineages. The characteristics of K. pneumoniae may impact the development of venom in venomous snakes.

CONCLUSION

The results of the native microbiome in the oral cavity and skin of newborn P. mucrosquamatus demonstrated that the habitat environment and prey capture may affect the composition of bacteria in adult snakes. We hypothesized that the native microbiome influences newborn venomous snakes and that K. pneumoniae lineages related to citrate fermentation may play a role in venom growth. However, further verification of this is required.