Draft Genome Sequence of Bacillus alcalophilus AV1934, a Classic Alkaliphile Isolated from Human Feces in 1934

Evaluating the Bacterial Diversity from the Southwest Coast of India Using Fatty Acid Methyl Ester Profiles

The fatty acid composition of bacterial isolates remains stable under standardized culture conditions, which makes it a useful taxonomic marker. The present study aims to characterize the diversity and quantity of fatty acid methyl esters (FAME) profiles of cultivable bacterial isolates collected along the southwest coast of India. Based on the similarity indices (range > 0.3-0.7) of the FAME profiles, the isolates were aggregated into 10 families, 11 genera and 19 species of cultured isolates. The following classes of bacteria were found: Bacilli, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Actinobacteria, which also included a few pathogens such as Pseudomonas, Staphylococcus and Bacillus sp. The hydroxyl FAMEs 2-hydroxydodecanoic acid (C_12:0 2OH), 2-hydroxypentadecanoic acid (C_15:0 2OH),3-hydroxy 14-methylpentadecanoic acid (C_16:0iso 3OH), 3 hydroxy hexadecenoic acid (C_16:0 3OH) and 3-hydroxy 15-methylhexadecanoic acid (C_17:0iso 3OH), as well as the unsaturated FAMEs (11Z)-11-hexadecenoic acid (C_16:1 ɷ5c), were exclusively associated with the isolates from Mangalore samples. Similarly, FAMEs 2-hydroxydecanoic acid (C_10:0 2OH), 9-methyldecanoic acid (C_11:0iso), undecanoic acid (C_11:0), tridecanoic acid (C_13:0), 10-methylhexadecanoic acid (C_16:0 10-CH₃) and (7Z)-7-hexadecenoic acid (C_16:1 ɷ9c) occurred only in the isolates from Trivandrum samples. However, the isolates from Goa did not possess a signature FAME profile. The reproducibility of the GC-MIDI bacterial identification system was evaluated using 16S rRNA gene sequencing techniques for selected isolates.

MotP Subunit is Critical for Ion Selectivity and Evolution of a K+-Coupled Flagellar Motor

The bacterial flagellar motor is a sophisticated nanomachine embedded in the cell envelope. The flagellar motor is driven by an electrochemical gradient of cations such as H⁺, Na⁺, and K⁺ through ion channels in stator complexes embedded in the cell membrane. The flagellum is believed to rotate as a result of electrostatic interaction forces between the stator and the rotor. In bacteria of the genus Bacillus and related species, the single transmembrane segment of MotB-type subunit protein (MotB and MotS) is critical for the selection of the H⁺ and Na⁺ coupling ions. Here, we constructed and characterized several hybrid stators combined with single Na⁺-coupled and dual Na⁺- and K⁺-coupled stator subunits, and we report that the MotP subunit is critical for the selection of K⁺. This result suggested that the K⁺ selectivity of the MotP/MotS complexes evolved from the single Na⁺-coupled stator MotP/MotS complexes. This finding will promote the understanding of the evolution of flagellar motors and the molecular mechanisms of coupling ion selectivity.

Nonconventional cation-coupled flagellar motors derived from the alkaliphilic Bacillus and Paenibacillus species

Prior to 2008, all previously studied conventional bacterial flagellar motors appeared to utilize either H⁺ or Na⁺ as coupling ions. Membrane-embedded stator complexes support conversion of energy using transmembrane electrochemical ion gradients. The main H⁺-coupled stators, known as MotAB, differ from Na⁺-coupled stators, PomAB of marine bacteria, and MotPS of alkaliphilic Bacillus. However, in 2008, a MotAB-type flagellar motor of alkaliphilic Bacillus clausii KSM-K16 was revealed as an exception with the first dual-function motor. This bacterium was identified as the first bacterium with a single stator-rotor that can utilize both H⁺ and Na⁺ for ion-coupling at different pH ranges. Subsequently, another exception, a MotPS-type flagellar motor of alkaliphilic Bacillus alcalophilus AV1934, was reported to utilize Na⁺ plus K⁺ and Rb⁺ as coupling ions for flagellar rotation. In addition, the alkaline-tolerant bacterium Paenibacillus sp. TCA20, which can utilize divalent cations such as Ca²⁺, Mg²⁺, and Sr²⁺, was recently isolated from a hot spring in Japan, which contains a high Ca²⁺ concentration. These findings show that bacterial flagellar motors isolated from unique environments utilize unexpected coupling ions. This suggests that bacteria that grow in different extreme environments adapt to local conditions and evolve their motility machinery.

Alkaliphilic Bacteria with Impact on Industrial Applications, Concepts of Early Life Forms, and Bioenergetics of ATP Synthesis

Alkaliphilic bacteria typically grow well at pH 9, with the most extremophilic strains growing up to pH values as high as pH 12–13. Interest in extreme alkaliphiles arises because they are sources of useful, stable enzymes, and the cells themselves can be used for biotechnological and other applications at high pH. In addition, alkaline hydrothermal vents represent an early evolutionary niche for alkaliphiles and novel extreme alkaliphiles have also recently been found in alkaline serpentinizing sites. A third focus of interest in alkaliphiles is the challenge raised by the use of proton-coupled ATP synthases for oxidative phosphorylation by non-fermentative alkaliphiles. This creates a problem with respect to tenets of the chemiosmotic model that remains the core model for the bioenergetics of oxidative phosphorylation. Each of these facets of alkaliphilic bacteria will be discussed with a focus on extremely alkaliphilic Bacillus strains. These alkaliphilic bacteria have provided a cogent experimental system to probe adaptations that enable their growth and oxidative phosphorylation at high pH. Adaptations are clearly needed to enable secreted or partially exposed enzymes or protein complexes to function at the high external pH. Also, alkaliphiles must maintain a cytoplasmic pH that is significantly lower than the pH of the outside medium. This protects cytoplasmic components from an external pH that is alkaline enough to impair their stability or function. However, the pH gradient across the cytoplasmic membrane, with its orientation of more acidic inside than outside, is in the reverse of the productive orientation for bioenergetic work. The reversed gradient reduces the trans-membrane proton-motive force available to energize ATP synthesis. Multiple strategies are hypothesized to be involved in enabling alkaliphiles to circumvent the challenge of a low bulk proton-motive force energizing proton-coupled ATP synthesis at high pH.