Characterization and genomic analysis of Exiguobacterium alkaliphilum B-3531D, an efficient crude oil degrading strain

Cold-adapted Exiguobacterium sibiricum K1 as a potential bioinoculant in cold regions: Physiological and genomic elucidation of biocontrol and plant growth promotion

The scarcity of soil nutrient availability under cold conditions of Himalayan regions needs a sustainable approach for better crop yields. The cold-adapted bacteria, Exiguobacterium sibiricum K1, with the potential to produce several plant growth-promoting (PGP) attributes, nitrogen fixation, indole acetic acid production, phosphate and potassium solubilization at 10 °C can provide an opportunity to promote crop yield improvement in an eco-friendly way under cold conditions. The bacterium also exhibited biocontrol activity against two phytopathogens and produced siderophore (53.0 ± 0.5 % psu). The strain's PGP properties were investigated using a spinach-based bioassay under controlled conditions. The bacterized seeds showed a notable increase in germination rate (23.2 %), shoot length (65.3 %), root length (56.6 %), leaf area (73.7 %), number of leaflets (65.2 %), and dry matter (65.2 %). Additionally, the leaf analysis indicated elevated chlorophyll pigments, i.e., chlorophyll a (55.5 %), chlorophyll b (42.8 %), carotenoids (35.2 %), percentage radical scavenging activity (47.4 %), and leaf nutrient uptake such as nitrogen (23.4 %), calcium (60.8 %), potassium (62.3 %), and magnesium (28.9 %). Moreover, the whole-genome sequencing and genome mining endorsed various biofertilisation-related genes, including genes for potassium and phosphate solubilization, iron and nitrogen acquisition, carbon dioxide fixation, and biocontrol ability of Exiguobacterium sibiricum K1. Overall, this study highlights the role of Exiguobacterium sibiricum K1 as a potential bioinoculant for improving crop yield under cold environments.

Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group

Delineating cohesive ecological units and determining the genetic basis for their environmental adaptation are among the most important objectives in microbiology. In the last decade, many studies have been devoted to characterizing the genetic diversity in microbial populations to address these issues. However, the impact of extreme environmental conditions, such as temperature and salinity, on microbial ecology and evolution remains unclear so far. In order to better understand the mechanisms of adaptation, we studied the (pan)genome of Exiguobacterium, a poly-extremophile bacterium able to grow in a wide range of environments, from permafrost to hot springs. To have the genome for all known Exiguobacterium type strains, we first sequenced those that were not yet available. Using a reverse-ecology approach, we showed how the integration of phylogenomic information, genomic features, gene and pathway enrichment data, regulatory element analyses, protein amino acid composition, and protein structure analyses of the entire Exiguobacterium pangenome allows to sharply delineate ecological units consisting of mesophilic, psychrophilic, halophilic-mesophilic, and halophilic-thermophilic ecotypes. This in-depth study clarified the genetic basis of the defined ecotypes and identified some key mechanisms driving the environmental adaptation to extreme environments. Our study points the way to organizing the vast microbial diversity into meaningful ecologically units, which, in turn, provides insight into how microbial communities adapt and respond to different environmental conditions in a changing world.

Iron-based multi-carbon composite and Pseudomonas furukawaii ZS1 co-affect nitrogen removal, microbial community dynamics and metabolism pathways in low-temperature aquaculture wastewater

Aerobic denitrification is the key process in the elimination of nitrogen from aquaculture wastewater, especially for wastewater with high dissolved oxygen and low carbon/nitrogen (C/N) ratio. However, a low C/N ratio, especially in low-temperature environments, restricts the activity of aerobic denitrifiers and decreases the nitrogen elimination efficiency. In this study, an iron-based multi-solid carbon source composite that immobilized aerobic denitrifying bacteria ZS1 (IMCSCP) was synthesized to treat aerobic (DO > 5 mg/L), low temperature (<15 °C) and low C/N ratio (C/N = 4) aquaculture wastewater. The results showed that the sequencing batch biofilm reactor (SBBR) packed with IMCSCP exhibited the highest nitrogen removal performance, with removal rates of 95.63% and 85.44% for nitrate nitrogen and total nitrogen, respectively, which were 33.03% and 30.75% higher than those in the reactor filled with multi-solid carbon source composite (MCSC). Microbial community and network analysis showed that Pseudomonas furukawaii ZS1 successfully colonized the SBBR filled with IMCSCP, and Exiguobacterium, Cellulomonas and Pseudomonas were essential for the nitrogen elimination. Metagenomic analysis showed that an increase in gene abundance related to carbon metabolism, nitrogen metabolism, extracellular polymer substance synthesis and electron transfer in the IMCSCP, enabling denitrification in the SBBR to be achieved via multiple pathways. The results of this study provided new insights into the microbial removal mechanism of nitrogen in SBBR packed with IMCSCP at low temperatures.

Study on potential microbial community to the waste water treatment from bauxite desilication process

Discharging waste water from the bauxite desilication process will bring potential environmental risk from the residual ions and organic compounds, especially hydrolyzed polyacrylamide. Characterization of the microbial community diversity in waste water plays an important role in the biological treatment of waste water. In this study, eight waste water samples from five flotation plants in China were investigated. The microbial community and functional profiles within the waste water were analyzed by a metagenomic sequencing method and associated with geochemical properties. The results revealed that Proteobacteria and Firmicutes were the dominant bacterial phyla. Both phylogenetical and clusters of orthologous groups' analyses indicated that Tepidicella, Paracoccus, Pseudomonas, and Exiguobacterium could be the dominant bacterial genera in the waste water from bauxite desilication process for their abilities to biodegrade complex organic compounds. The results of the microbial community diversity and functional gene compositions analyses provided a beneficial orientation for the biotreatment of waste water, as well as regenerative using of water resources. Besides, this study revealed that waste water from bauxite desilication process was an ideal ecosystem to find novel microorganisms, such as efficient strains for bio-desilication and bio-desulfurization of bauxite.

Using Biological Responses to Monitor Freshwater Post-Spill Conditions over 3 years in Blacktail Creek, North Dakota, USA

A pipeline carrying unconventional oil and gas (OG) wastewater spilled approximately 11 million liters of wastewater into Blacktail Creek, North Dakota, USA. Flow of the mix of stream water and wastewater down the channel resulted in storage of contaminants in the hyporheic zone and along the banks, providing a long-term source of wastewater constituents to the stream. A multi-level investigation was used to assess the potential effects of oil and brine spills on aquatic life. In this study, we used a combination of experiments using a native fish species, Fathead Minnow (Pimephales promelas), field sampling of the microbial community structure, and measures of estrogenicity. The fish investigation included in situ experiments and experiments with collected site water. Estrogenicity was measured in collected site water samples, and microbial community analyses were conducted on collected sediments. During the initial post-spill investigation, February 2015, performing in situ fish bioassays was impossible because of ice conditions. However, microbial community (e.g., the presence of members of the Halomonadaceae, a family that is indicative of elevated salinity) and estrogenicity differences were compared to reference sites and point to early biological effects of the spill. We noted water column effects on in situ fish survival 6 months post-spill during June 2015. At that time, total dissolved ammonium (sum of ammonium and ammonia, TAN) was 4.41 mg NH₄/L with an associated NH₃ of 1.09 mg/L, a concentration greater than the water quality criteria established to protect aquatic life. Biological measurements in the sediment defined early and long-lasting effects of the spill on aquatic resources. The microbial community structure was affected during all sampling events. Therefore, sediment may act as a sink for constituents spilled and as such provide an indication of continued and cumulative effects post-spill. However, lack of later water column effects may reflect pulse hyporheic flow of ammonia from shallow ground water. Combining fish toxicological, microbial community structure and estrogenicity information provides a complete ecological investigation that defines potential influences of contaminants at organismal, population, and community levels. In general, in situ bioassays have implications for the individual survival and changes at the population level, microbial community structure defines potential changes at the community level, and estrogenicity measurements define changes at the individual and molecular level. By understanding effects at these various levels of biological organization, natural resource managers can interpret how a course of action, especially for remediation/restoration, might affect a larger group of organisms in the system. The current work also reviews potential effects of additional constituents defined during chemistry investigations on aquatic resources.

Synchronous microbial V(V) reduction and denitrification using corn straw as the sole carbon source

The coexistence of nitrate and V(V) in groundwater aquifers poses potential threats to ecological environment and public health. However, much remains to be elucidated about how the complex microbial community coupled nitrate and V(V) simultaneous bio-reduction with carbon source oxidation. For the first time, it was demonstrated that denitrification and V(V) bio-reduction occur by using corn straw as the sole carbon and energy source. Corn straw was proved to have efficient denitrification and V(V) bio-reduction performance in various environments, especially at V(V) concentrations of 100 mg/L for optimal V(V) reduction rate (19.25 mg/L·d) and at pH of 11 with the best nitrate reduction rate (3.12 d^-1). In addition, an interesting phenomenon was found that the release of V(V) occurred when the carbon source was insufficient and the competitive electron acceptor (NO₃^--N) existed. Metagenomic analysis showed that the addition of corn straw increased the abundance of genes related to metal resistance, cytochrome and dimethyl sulfoxide, and increased the abundance of glycolytic process, which may play a vital role in facilitating the reduction of V(V). These findings can provide basic suggestions for improving the mechanism of V(V) reduction pathway and provide guidance for the remediation of groundwater polluted by nitrate and V(V).

Study of the Ca2+-dependent gene expression of EuPrt, an extracellular metalloprotease produced by the psychro-tolerant bacterium Exiguobacterium undae Su-1

The effect of a Ca2+ ion on the gene expression of an on-demand type of metalloprotease from psychrotrophic Exiguobacterium undae Su-1 (EuPrt) was studied. We first established a modified mM9 medium for strain Su-1 to examine its effect in more detail. Then, when the strain was cultured in mM9 medium and 1.0 mM CaCl2 was added, we detected the mature EuPrt and its precursor proteins via Western blotting analysis and found the relative protease activity and its transcription increased by 50-fold and 7-fold, respectively, at the peak. Furthermore, the intracellular concentration of Ca2+ ions was analyzed using inductively coupled plasma atomic emission spectroscopy (ICP-AES) with other metal ions along the growth of strain Su-1. The intracellular concentration of Ca2+ ion was found to increase as much as 3-fold in response to the addition of an extracellular Ca2+ ions, indicating that euPrt gene expression is regulated by sensing its intracellular concentration.