Bacterial Diversity in the Metal-Rich Terrestrial Deep Subsurface Sediments of Krishna Godavari Basin,India

Abstract

Krishna Godavari (KG) basin, located in the eastern continental margin of India, is a geological region well known for the abundance of economically important minerals. However, less is known about the microbial ecology of its subsurface sediments. The present study is the first report on the comprehensive culture-independent census of bacterial communities of deep subsurface of KG basin and their relationship with the geochemical environment. Elemental and mineralogical characterization of the sediments highlighted the presence of carbon and nitrogen deprived conditions along with the abundance of metalliferous minerals, especially rich in valuable elements like zirconium, vanadium, cesium, and rare earth elements. Diversity analysis based on Illumina MiSeq high-throughput sequencing platform revealed the predominance of Firmicutes (44.24%), Proteobacteria (34.17%), Bacteroidetes (15.18%), and Actinobacteria (3.81%) in the deep subsurface of this basin. ‘Abundant’ and ‘rare’ sub-communities analysis indicated that a large number of phyla like Acidobacteria, Armatimonadetes, Chloroflexi, and Deinococcus-Thermus were exclusively present as a rare community. Statistical analyses demonstrated that geochemical parameters, especially depth, pH, and metal content, showed significant influence on the microbial community structure. The present study should help future investigations for microbial mediated sustainable utilization of mineral-rich sediments of the region.     

Ecology, physiology, and phylogeny of deep subsurface Sphingomonas sp

Several new species of the genus Sphingomonas including S. aromaticivorans, S. stygia, and S. subterranea that have the capacity for degrading a broad range of aromatic compounds including toluene, naphthalene, xylenes, p-cresol, fluorene, biphenyl, and dibenzothiophene, were isolated from deeply-buried (>200 m) sediments of the US Atlantic coastal plain (ACP). In S. aromaticivorans F199, many of the genes involved in the catabolism of these aromatic compounds are encoded on a 184-kb conjugative plasmid; some of the genes involved in aromatic catabolism are plasmid-encoded in the other strains as well. Members of the genus Sphingomonas were common among aerobic heterotrophic bacteria cultured from ACP sediments and have been detected in deep subsurface environments elsewhere. The major source of organic carbon for heterotrophic metabolism in ACP deep aquifers is lignite that originated from plant material buried with the sediments. We speculate that the ability of the subsurface Sphingomonas strains to degrade a wide array of aromatic compounds represents an adaptation for utilization of sedimentary lignite. These and related subsurface Sphingomonas spp may play an important role in the transformation of sedimentary organic carbon in the aerobic and microaerobic regions of the deep aquifers of the ACP. Received 12 May 1999/ Accepted in revised form 25 July 1999     

Climate warming alters subsoil but not topsoil carbon dynamics in alpine grassland

Subsoil contains more than half of soil organic carbon (SOC) globally and is conventionally assumed to be relatively unresponsive to warming compared to the topsoil. Here, we show substantial changes in carbon allocation and dynamics of the subsoil but not topsoil in the Qinghai‐Tibetan alpine grasslands over 5 years of warming. Specifically, warming enhanced the accumulation of newly synthesized (¹⁴C‐enriched) carbon in the subsoil slow‐cycling pool (silt‐clay fraction) but promoted the decomposition of plant‐derived lignin in the fast‐cycling pool (macroaggregates). These changes mirrored an accumulation of lipids and sugars at the expense of lignin in the warmed bulk subsoil, likely associated with shortened soil freezing period and a deepening root system. As warming is accompanied by deepening roots in a wide range of ecosystems, root‐driven accrual of slow‐cycling pool may represent an important and overlooked mechanism for a potential long‐term carbon sink at depth. Moreover, given the contrasting sensitivity of SOC dynamics at varied depths, warming studies focusing only on surface soils may vastly misrepresent shifts in ecosystem carbon storage under climate change.     

Molecular docking analysis of azithromycin and hydroxychloroquine with spike surface glycoprotein of SARS-CoV-2

Millions of people are affected by COVID-19 since the last quarter of 2019. Treatment using hydroxychloroquine (HCQ) as monotherapy in combination with azithromycin (HCQ-AZ) were administered at several clinical centres to patients tested positive to the virus across continents. Therefore, it is of interest to document the molecular docking analysis data of azithromycin and hydroxychloroquine drug with the spike surface glycoprotein of novel COVID-19. Thus, we report the molecular modelling docking based structural binding features of HCQ-AZ with the spike surface glycoprotein of COVID-19 for further evaluation in this regard.     

Building and breeding molecules to spy on cells and tumors

Imaging of biochemical processes in living cells and organisms is essential for understanding how genes and gene products work together in space and time and in health and disease. Such imaging depends crucially on indicator molecules designed to maximize sensitivity and specificity. These molecules can be entirely synthetic, entirely genetically encoded macromolecules, or hybrid combinations, each approach having its own pros and cons. Recent examples from the author's laboratory include peptides whose uptake into cells is triggered by proteases typical of tumors, monomeric red fluorescent proteins and biarsenical-tetracysteine systems for determining the age and electron-microscopic location of proteins.     

Continuous culture with deep seawater of a benthic food diatom Nitzschia sp.

A continuous culture system for a benthic food diatom Nitzschia sp. wasestablished by using properties of high nutrient and clean of deep seawater(DSW). DSW collected from 320 m depth in Muroto City, Japan, was introducedinto a glass-pipe bioreactor (14 cm length, 3 cm diam.) containing glassbeads of 0.5 cm diam. as substrata for the alga, and it was incubated at18°C · 80Em^–2sec^–1 · L:D=14:10. The chlorophyll a yield of benthicdiatoms in a reactor as a unit of surface area of the substratum was only0.001–0.003 g cm^–2 when the flow rate of DSW was 0(batch culture conditions). However, when DSW was supplied continuously to areactor, the yield increased to 1.4 g-chl.a cm^–2 alongwith the increase in flow rate of DSW. Moreover, amounts of chl.a washed outof the system were negligible, 0.0014 to 0.0045%, even though theflow rate of DSW was as much as 25 times h^–1, suggesting thatsloughing of benthic diatoms from the substratum was minimized. Although theyield of diatoms fluctuated significantly at the time that the DSW wascollected, the variation could be minimized by increasing the flow rate ofDSW. These results indicate that the continuous culturing system with DSWsupports the stable and effective mass culture of benthic food diatom.     

Trypanosoma brucei: Maintenance of concentrated suspensions of bloodstream trypomastigotes in vitro using continuous dialysis for measurement of endocytosis

A continuous dialysis technique capable of maintaining concentrated suspensions of bloodstream Trypanosoma brucei (up to 4 × 10⁸/ml) at 25 C for 2 hr without loss of viability has been developed in order to measure endocytosis under controlled conditions in vitro. Using this technique, the kinetics and mechanism of uptake of the metabolically inert macromolecule, ¹²⁵I-labelled polyvinylpyrrolidone (¹²⁵I-PVP), have been investigated. Binding to the plasma membrane and the rate of uptake of ¹²⁵I-PVP from the extracellular medium by the trypanosome are both decreased by the addition of unlabelled PVP and human serum albumin. A mechanism for uptake of ¹²⁵I-PVP by a combination of fluid-phase and adsorptive endocytosis from the flagellar pocket of the trypanosome is proposed. In the presence of serum albumin and unlabelled PVP, endocytosis of ¹²⁵I-PVP occurs in the fluid phase only, with endocytic indices of 14.5 ± 0.9 and 54.1 ± 11.3 nl/hr/mg protein in vitro at 25 C and in vivo at 37 C, respectively.     

Structure and growth pattern of the bizarre hemispheric prominence on the rostrum of the fossil beaked whale Globicetus hiberus (Mammalia,Cetacea, Ziphiidae)

The rostrum of most ziphiids (beaked whales) displays bizarre swollen regions, accompanied with extreme hypermineralisation and an alteration of the collagenous mesh of the bone. The functional significance of this specialization remains obscure. With the voluminous and dense hemispheric excrescence protruding from the premaxillae, the recently described fossil ziphiid Globicetus hiberus is the most spectacular case. This study describes the histological structure and interprets the growth pattern of this unique feature. Histologically, the prominence in Globicetus is made up of an atypical fibro‐lamellar complex displaying an irregular laminar organization and extreme compactness (osteosclerosis). Its development is suggested to have resulted from a protraction of periosteal accretion over the premaxillae, long after the end of somatic growth. Complex shifts in the geometry of this tissue are likely to have occurred during its accretion and no indication of Haversian remodeling could be found. X‐ray diffraction and Raman spectroscopy indicate that the bone matrix in the premaxillary prominence of Globicetus closely resembles that of the rostrum of the extant beaked whale Mesoplodon densirostris: apatite crystals are of common size and strongly oriented, but the collagenous meshwork within bone matrix seems to be extremely sparse. These morphological and structural data are discussed in the light of functional interpretations proposed for the highly unusual and diverse ziphiid rostrum. J. Morphol. 277:1292–1308, 2016. © 2016 Wiley Periodicals, Inc.     

深挖垦复对锥栗重要农艺性状及土壤理化性质的影响

为探索锥栗林地高效的土壤管理方式,提升我国锥栗栽培管理技术水平,进而提高其产量、品质以及经济效益。该研究采用全垦和环垦两种方式对锥栗林地进行连续4年的深挖垦复,通过测定垦复前后土壤理化性质变化以及锥栗树体生长、叶片表型和生理特征、结果性状、产量及品质等重要农艺性状,统计数据并进行对比分析。结果表明:(1)深挖垦复对锥栗林地土壤理化性质改善效果显著,两种垦复方式土壤容重较垦复前降低31.21%及以上(0～30 cm处),土壤含水率、土壤孔隙度、有机质含量以及各种大量元素含量较垦复前和对照均有不同程度的增加,土壤肥力及其保水保肥能力显著增强。(2)环垦区土壤有机质含量、有效磷含量以及交换性镁含量高于全垦区,其土壤有机质含量较垦复前增加40.59%,远高于全垦增加幅度(17.76%),从土壤保肥能力的角度来看,环垦效果优于全垦。(3)土壤肥力的提升增强了其对锥栗叶片的供肥能力,使得叶片含水率、叶绿素含量以及各种矿质元素含量显著增加,从而提升其光合作用能力。(4)深挖垦复对锥栗树体生长、结实能力、产量及品质同样具有显著的提升效果,其中全垦和环垦区单位面积产量分别是对照的1.75倍和1.33倍,且栗苞总重、单果质量、出籽率、可溶性糖含量以及磷、钾元素含量显著高于对照,而空苞率显著低于对照。综上,深挖垦复是改良林地土壤和提高锥栗生产力的有效举措。