Biodeterioration of Mayan buildings at uxmal and tulum,Mexico

Uxmal and Tulum are two important Mayan sites in the Yucatan peninsula. The buildings are mainly composed of limestone and grey/black discoloration is seen on exposed walls and copious greenish biofilms on inner walls. The principal microorganisms detected on interior walls at both Uxmal and Tulum were cyanobacteria; heterotrophic bacteria and filamentous fungi were also present. A dark‐pigmented mitosporic fungus and Bacillus cereus, both isolated from Uxmal, were shown to be acidogenic in laboratory cultures. Cyanobacteria belonging to rock‐degrading genera Synechocystis and Gloeocapsa were identified at both sites. Surface analysis previously showed that calcium ions were present in the biofilms on buildings at Uxmal and Tulum, suggesting the deposition of biosolubilized stone. Apart from their potential to degrade the substrate, the coccoid cyanobacteria supply organic nutrients for bacteria and fungi, which can produce organic acids, further increasing stone degradation.     

Isolation and characterization of plant growth-promoting strain Pantoea NII-186. From Western Ghat Forest soil, India

Aims:  To isolate plant growth-promoting bacterium from Western Ghat forests in India.
Methods and Results:  A Gram-negative, rod shaped, cream white coloured strain Pantoea NII-186 isolated from Western Ghat soil sample. The taxonomic position of the bacterium was confirmed by sequencing of 16S rRNA and phylogenetic analysis. A strain grew at a wide range of temperature ranging from 5–40°C, but optimum growth was observed at 28–30°C. It showed multiple plant growth-promoting attributes such as phosphate solubilization activity, indole acetic acid (IAA) production, siderophore production and HCN production. It was able to solubilize (28 μg of Ca₃PO₄ ml⁻¹ day⁻¹), and produce IAA (59 μg) at 28°C. The solubilization of insoluble phosphate was associates with a drop in the pH of the culture medium. Pantoea sp. NII-186 tolerate to different environmental stresses like 5–40°C, 0–7% salt concentration and 4–12 pH range.
Conclusions:  The 16S rRNA gene sequence confirmed that the isolate NII-186 was belongs to Pantoea genus and showed considerable differences in physiological properties with previously reported species of this genus. Isolate NII-186 possessed multiple attributes of plant growth-promoting activity.
Significance and Impact of the Study:  Hence in the context it is proposed that Pantoea sp. NII-186, could be deployed as an inoculant to attain the desired plant growth-promoting activity in agricultural environment.     

Bacillus enclensis sp. nov., isolated from sediment sample

A novel bacterial strain, designated SGD-1123^T was isolated from Chorao Island, in Goa Province, India. The strain was found to be able to grow at 15–42 °C, pH 5–12 and 0–12 % (w/v) NaCl. The whole cell hydrolysates were found to contain meso-diaminopimelic acid, galactose and arabinose. The major fatty acids were identified as iso-C_15:0 and anteiso-C_15:0, MK-7 was identified as the predominant menaquinone and the predominant polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminolipid. The genomic DNA G+C content was determined to be 44.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolate within the genus Bacillus and further revealed that strain SGD-1123^T had highest sequence similarity with Bacillus aquimaris, and forms a separate clade with its closest relatives i.e. B. aquimaris, Bacillus vietnamensis and Bacillus marisflavi, with which it shares 94.5, 94.1 and 94.1 % similarity respectively. The phylogenetic, chemotaxonomic and phenotypic analyses indicated that strain SGD-1123^T represents a novel species within the genus Bacillus, for which the name Bacillus enclensis is proposed. The type strain is SGD-1123^T (NCIM 5450^T=CCTCC AB 2011125^T).     

Plant growth-promoting activity in newly isolated <Emphasis Type="Italic">Bacillus thioparus</Emphasis> (NII-0902) from Western <Emphasis Type="Italic">ghat</Emphasis> forest,India

A Gram-positive rod-shaped bacterium isolated on nutrient agar plates incubated at 28 ± 2°C. The identity of the bacterium was confirmed by sequencing of the 16S rRNA gene and it reveals that it shares highest similarity with Bacillus thioparus CECT 7196^T (99.08%). It was capable of growing at temperatures ranging from 4 to 40°C, but optimum growth was observed at 28 ± 2°C. Strain NII-0902 is endowed with multiple plant growth promotion attributes such as phosphate solubilization, Indole acetic acid (IAA), siderophore and HCN production, which were expressed differentially at sub-optimal temperatures (5–40°C). It was able to solubilize phosphate (17.7 μg ml⁻¹), and produce IAA (139.7 μg ml⁻¹) at 28 ± 2°C. Qualitative detection of siderophore production and HCN were also observed. At 5°C it was found to express all the plant growth promotion attributes except HCN production. The ability to colonize roots is a sine qua non condition for a rhizobacteria to be considered a true plant growth-promoting rhizobacteria (PGPR). Bacillus sp. NII-0902 has a potential ability to colonize roots visualized by transparency, bacterial growth (turbid, milky and narrow zone) along and around roots and truly supported by scanning electron micrograph. Hence, it is proposed that, Bacillus thioparus sp. NII-0902 could be deployed as an inoculant to attain the desired results of bacterization.     

Proteolytic Activity from an Alkali-Thermotolerant <Emphasis Type="Italic">Streptomyces gulbargensis</Emphasis> sp. nov.

Multiple proteases were produced and partially purified from an alkali-thermotolerant novel species of Streptomyces (i.e., Streptomyces gulbargensis DAS 131) after 48 h of growth at 45°C. The enzyme preparation exhibited activity over a broad range of pH (4–12) and temperature (27–55°C). Optimum activity was observed at a pH of 9.0 and a temperature of 45°C. Starch and protease peptone was found to be a good source of carbon and nitrogen to enhance the enzyme activity. Two active zones in the range of 19 to 35 kDa were detected on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE).     

Terrigenous sediment-dominated reef platform infilling: an unexpected precursor to reef island formation and a test of the reef platform size–island age model in the Pacific

Low-lying coral reef islands are considered highly vulnerable to climate change, necessitating an improved understanding of when and why they form, and how the timing of formation varies within and among regions. Several testable models have been proposed that explain inter-regional variability as a function of sea-level history and, more recently, a reef platform size model has been proposed from the Maldives (central Indian Ocean) to explain intra-regional (intra-atoll) variability. Here we present chronostratigraphic data from Pipon Island, northern Great Barrier Reef (GBR), enabling us to test the applicability of existing regional island evolution models, and the platform size control hypothesis in a Pacific context. We show that reef platform infilling occurred rapidly (~4–5 mm yr⁻¹) under a “bucket-fill” type scenario. Unusually, this infilling was dominated by terrigenous sedimentation, with platform filling and subsequent reef flat formation complete by ~5000 calibrated years BP (cal BP). Reef flat exposure as sea levels slowly fell post highstand facilitated a shift towards intertidal and subaerial-dominated sedimentation. Our data suggest, however, a lag of ~1500 yr before island initiation (at ~3200 cal BP), i.e. later than that reported from smaller and more evolutionarily mature reef platforms in the region. Our data thus support: (1) the hypothesis that platform size acts to influence the timing of platform filling and subsequent island development at intra-regional scales; and (2) the hypothesis that the low wooded islands of the northern GBR conform to a model of island formation above an elevated reef flat under falling sea levels.

     

Polyphasic Taxonomy of Novel Actinobacteria Showing Macromolecule Degradation Potentials in Bigeum Island,Korea

Aerobic, alkaliphilic to alkalitolerant and mesophilic bacteria were isolated and characterized from soil and sediment samples collected from Bigeum Island, South Korea. The total numbers of microorganisms in the soil and sediment samples were found to be 10³–10⁵ cfu/g and 10²–10⁷ cfu/g, respectively. A total of 163 isolates were isolated and subjected to further characterization on the basis of pH, temperature and salt tolerance. Among the 163 isolates, 54 were selected based on their tolerance attributes to temperature, pH and NaCl. Out of the 54 isolates, 27 were further selected based on their multiple tolerance ability and enzyme profile and were subjected to 16S rRNA gene sequencing and phylogenetic analysis. The latter indicated that most of the Bigeum Island isolates were related to the phylum Actinobacteria. The phylogenetic tree based on 16S rRNA gene sequences placed the 27 isolates into 9 different major bacterial genera, each genus comprising pure cultures that shared ≤97% sequence identity and 18 putative novel species. Most of the strains were alkalitolerant and mesophilic, and produced biotechnologically important enzymes at alkaline pH.     

Methylated DNA/RNA in Body Fluids as Biomarkers for Lung Cancer

DNA/RNA methylation plays an important role in lung cancer initiation and progression. Liquid biopsy makes use of cells, nucleotides and proteins released from tumor cells into body fluids to help with cancer diagnosis and prognosis. Methylation of circulating tumor DNA (ctDNA) has gained increasing attention as biomarkers for lung cancer. Here we briefly introduce the biological basis and detection method of ctDNA methylation, and review various applications of methylated DNA in body fluids in lung cancer screening, diagnosis, prognosis, monitoring and treatment prediction. We also discuss the emerging role of RNA methylation as biomarkers for cancer.     

Growth enhancement of black pepper (<Emphasis Type="Italic">Piper nigrum</Emphasis>) by a newly isolated <Emphasis Type="Italic">Bacillus tequilensis</Emphasis> NII-0943

A Gram positive, rod-shaped potential strain was selected from the pool of bacterial isolates obtained from the Western Ghats forest (India) on the basis of zone of P-solubilization activity. Identification based on 16S rRNA gene sequence revealed that the strain is of Bacillus species, sharing highest sequence similarity to Bacillus tequilensis NRRL B-41771^T (99.5%). Strain NII-0943 was able to produce good amount of indole acetic acid (IAA) and was positive for siderophore production. In addition to IAA and siderophore attributes, strain NII-0943 also possessed the characteristics like Ca₃(PO₄)₂ solubilization and growth in nitrogen-free medium. Seed inoculation with the strain NII-0943 resulted in significantly higher root initiation in black pepper cuttings grown under pots. The contents of nitrogen and phosphorus in both soil and plant were also enhanced significantly in treatments inoculated with these bacterial inocula. Hence, based on this evidence it is proposed that strain NII-0943 could be deployed as a plant growth-promoting inoculant to attain the desired results of bacterization.     

Genetic Admixture in the Culturally Unique Peranakan Chinese Population in Southeast Asia

The Peranakan Chinese are culturally unique descendants of immigrants from China who settled in the Malay Archipelago ∼300–500 years ago. Today, among large communities in Southeast Asia, the Peranakans have preserved Chinese traditions with strong influence from the local indigenous Malays. Yet, whether or to what extent genetic admixture co-occurred with the cultural mixture has been a topic of ongoing debate. We performed whole-genome sequencing (WGS) on 177 Singapore (SG) Peranakans and analyzed the data jointly with WGS data of Asian and European populations. We estimated that Peranakan Chinese inherited ∼5.62% (95% confidence interval [CI]: 4.76–6.49%) Malay ancestry, much higher than that in SG Chinese (1.08%, 0.65–1.51%), southern Chinese (0.86%, 0.50–1.23%), and northern Chinese (0.25%, 0.18–0.32%). A sex-biased admixture history, in which the Malay ancestry was contributed primarily by females, was supported by X chromosomal variants, and mitochondrial (MT) and Y haplogroups. Finally, we identified an ancient admixture event shared by Peranakan Chinese and SG Chinese ∼1,612 (95% CI: 1,345–1,923) years ago, coinciding with the settlement history of Han Chinese in southern China, apart from the recent admixture event with Malays unique to Peranakan Chinese ∼190 (159–213) years ago. These findings greatly advance our understanding of the dispersal history of Chinese and their interaction with indigenous populations in Southeast Asia.