Discovering the roles of subsurface microorganisms: Progress and future of deep biosphere investigation

The discovery of the marine “deep biosphere”—microorganisms living deep below the seafloor—is one of the most significant and exciting discoveries since the ocean drilling program began more than 40 years ago. Study of the deep biosphere has become a research frontier and a hot spot both for geological and biological sciences. Here, we introduce the history of the discovery of the deep biosphere, and then we describe the types of environments for life below the seafloor, the energy sources for the living creatures, the diversity of organisms within the deep biosphere, and the new tools and technologies used in this research field. We will highlight several recently completed Integrated Ocean Drilling Program Expeditions, which targeted the subseafloor deep biosphere within the crust and sediments. Finally, future research directions and challenges of deep biosphere investigation towards uncovering the roles of subsurface microorganisms will be briefly addressed.     

番红活菌染色技术的实验研究

为研究活体细菌着色的适宜条件,将普通变形杆菌、金黄色葡萄球菌、大肠杆菌和乳酸链球菌的培养物稀释至浓度为2×106CFU·mL-1,经不同浓度与作用时间的番红着色洗涤后,置于甘油-生理盐水中保存,采用平皿菌落计数法测定细菌的CFU.结果显示,与对照组相比,用0.25%番红染色时,细菌CFU无显著性差异(P＞0.05),染料浓度≥0.75%时,CFU有差异性(P＜0.05).染色时间在10min内CFU无显著性差异(P＞0.05).用30%甘油-生理盐水保存着色活体细菌,在60 h内活性无显著性差异(P＞0.05).由此表明番红染色法适用于活体细菌染色的形态学检测.     

The life span of the biosphere revisited

A decade ago, Lovelock and Whitfield raised the question of how much longer the biosphere can survive on Earth. They pointed out that, despite the current fossil-fuel induced increase in the atmospheric CO2 concentration, the long-term trend should be in the opposite direction: as increased solar luminosity warms the Earth, silicate rocks should weather more readily, causing atmospheric CO2 to decrease. In their model, atmospheric CO2 falls below the critical level for C3 photosynthesis, 150 parts per million (p.p.m.), in only 100 Myr, and this is assumed to mark the demise of the biosphere as a whole. Here, we re-examine this problem using a more elaborate model that includes a more accurate treatment of the greenhouse effect of CO2, a biologically mediated weathering parameterization, and the realization that C4 photosynthesis can persist to much lower concentrations of atmospheric CO2(<10 p.p.m.). We find that a C4-plant-based biosphere could survive for at least another 0.9 Gyr to 1.5 Gyr after the present time, depending respectively on whether CO2 or temperature is the limiting factor. Within an additional 1 Gyr, Earth may lose its water to space, thereby following the path of its sister planet, Venus.     

Low marine sulphate and protracted oxygenation of the Proterozoic biosphere

Progressive oxygenation of the Earth's early biosphere is thought to have resulted in increased sulphide oxidation during continental weathering, leading to a corresponding increase in marine sulphate concentration. Accurate reconstruction of marine sulphate reservoir size is therefore important for interpreting the oxygenation history of early Earth environments. Few data, however, specifically constrain how sulphate concentrations may have changed during the Proterozoic era (2.5-0.54 Gyr ago). Prior to 2.2 Gyr ago, when oxygen began to accumulate in the Earth's atmosphere, sulphate concentrations are inferred to have been <1 mM and possibly <200 microM, on the basis of limited isotopic variability preserved in sedimentary sulphides and experimental data showing suppressed isotopic fractionation at extremely low sulphate concentrations. By 0.8 Gyr ago, oxygen and thus sulphate levels may have risen significantly. Here we report large stratigraphic variations in the sulphur isotope composition of marine carbonate-associated sulphate, and use a rate-dependent model for sulphur isotope change that allows us to track changes in marine sulphate concentrations throughout the Proterozoic. Our calculations indicate sulphate levels between 1.5 and 4.5 mM, or 5-15 per cent of modern values, for more than 1 Gyr after initial oxygenation of the Earth's biosphere. Persistence of low oceanic sulphate demonstrates the protracted nature of Earth's oxygenation. It links biospheric evolution to temporal patterns in the depositional behaviour of marine iron- and sulphur-bearing minerals, biological cycling of redox-sensitive elements and availability of trace metals essential to eukaryotic development.     

Direct observation of microtubule dynamics in living cells

The study of cell locomotion is fundamental to such diverse processes as embryonic development, wound healing and metastasis. Since microtubules play a role in establishing the leading lamellum and maintaining cell polarity, it is important to understand their dynamic behaviour. In vitro, subunits exchange with polymer by treadmilling and by dynamic instability. Disassembly events can be complete (catastrophic) or incomplete (tempered). In vivo, microtubules are in dynamic equilibrium with subunits with a half-time for turnover of 4-20 min. Microtubules grow by elongation of their ends and are replaced one by one with turnover being most rapid at the periphery. Although previous results are consistent with dynamic instability, we sought to directly test the mechanism of turnover. Direct observations of fluorescent microtubules in the fibroblast lamellum show that individual microtubules undergo rounds of assembly and disassembly from the same end. Reorganization of the microtubule network occurs by a tempered mode of dynamic instability.     

Subcellular localization of chitosan oligosaccharides in living cells

Chitosan oligosaccharides （COS） is derived from the chemical or enzymatic decomposition of chitosan. The exact mechanisms underlying many biological functions of COS have not been elucidated. Since subcellular localization is very important in determining biological activity in a number of molecules, we used fluorescein isothiocyanate-labeled chitosan oligosaccharides （FITC- COS） and investigated the localization of COS in living cells by laser scanning microscopy. We found that COS entered cells in a dose- and time-dependent manner, and we first showed that COS may enter cells by facilitated passive diffusion and was preferentially localized in the mitochondria. While in high concentration, it was also found in the cytoplasm and nucleus and was enriched in the nucleolus and karyotheca. The different subcellular localization of COS suggested that they played different effects. Determination of COS subcellular localization in cells is important to help us understand the potent mechanisms underlying its multiple functions.     

Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree

Although the relationship of angiosperms to other seed plants remains controversial, great progress has been made in identifying the earliest extant splits in flowering-plant phylogeny, with the discovery that the New Caledonian shrub Amborella trichopoda, the water lilies (Nymphaeales), and the woody Austrobaileyales constitute a basal grade of lines that diverged before the main radiation in the clade. By focusing attention on these ancient lines, this finding has re-written our understanding of angiosperm structural and reproductive biology, physiology, ecology and taxonomy. The discovery of a new basal lineage would lead to further re-evaluation of the initial angiosperm radiation, but would also be unexpected, as nearly all of the approximately 460 flowering-plant families have been surveyed in molecular studies. Here we show that Hydatellaceae, a small family of dwarf aquatics that were formerly interpreted as monocots, are instead a highly modified and previously unrecognized ancient lineage of angiosperms. Molecular phylogenetic analyses of multiple plastid genes and associated noncoding regions from the two genera of Hydatellaceae identify this overlooked family as the sister group of Nymphaeales. This surprising result is further corroborated by evidence from the nuclear gene phytochrome C (PHYC), and by numerous morphological characters. This indicates that water lilies are part of a larger lineage that evolved more extreme and diverse modifications for life in an aquatic habitat than previously recognized.     

复合菌剂处理深井聚磺钻井液废水技术研究

深井聚磺类钻井液废水中有机物含量高,可絮凝性差,降解难度大.开展了高效复合菌剂处理废水的技术研究,重点分析了复合菌剂优选、菌剂用量、曝气量等因素对处理效果的影响.结果表明:优势菌剂加量为0.5 g/L,曝气量为0.25 L/min,进水ρ(COD)<1 100 mg/L,污泥沉降比(SV)为25%～35%时,24 h后系统COD总去除率大于87%,处理后的水ρ(COD)≤150 mg/L,其他指标均达到《污水综合排放标准》的1级标准.     

Development of the CAS-IBB single-particle microbeam for localized irradiation of living cells

A single-particle microbeam facility has been constructed at the Key Laboratory of Ion Beam Bioengineering (LIBB), Chinese Academy of Sciences (CAS). The system was designed to deliver a defined numbers of hydrogen ions, produced by a van de Graaff accelerator, in an energy range of 2.0-3.0 MeV, into an area smaller than that of the nucleus of an individual living cell. The beam is collimated by a borosilicate glass capillary that forms the beam-line exit. An integrated computer program recognizes the cells and locates them one by one over the microbeam exit for irradiation. We present technical details of the CAS-LIBB microbeam facility, particularly on the collimator, hardware, control program, as well as cell irradiation protocols available. Various factors contributing to the targeting and positioning precision are discussed along with accuracy measurement results.     

Development of the CAS-LIBB single-particlemicrobeam for localizedirradiation of living cells

The use of microirradiation techniques in radiationbiology dates back to the work of Zirkle and his col-leagues in 1950’s[1,2]. However, biological effects of arandom single particle traversal in living materials re-mained highly unknown since they could not be simulatedby conventional broad-field radiation exposures. In recentyears, there has been a resurgence of interest in sin-gle-particle/single-cell microbeams[3—12]. The biologicalinterest in the single-particle microbeam stems from the…     

New discoveries on the state of hemoglobin in living red blood cells

Professor Qin Wenbin from BaoTou Medical College first identified the hemoglobin(Hb)A2phenomenon 30 years ago.His first paper onthis phenomenon was published in Acta Biochimica et Biophysica Sinica,in Chinese,in1981.Subsequent research investigating its mecha-nism was published in Chinese in the Chinese Biochemical Journal and Progress Biochimica     

Prokaryotic origin of the actin cytoskeleton.

It was thought until recently that bacteria lack the actin or tubulin filament networks that organize eukaryotic cytoplasm. However, we show here that the bacterial MreB protein assembles into filaments with a subunit repeat similar to that of F-actin-the physiological polymer of eukaryotic actin. By elucidating the MreB crystal structure we demonstrate that MreB and actin are very similar in three dimensions. Moreover, the crystals contain protofilaments, allowing visualization of actin-like strands at atomic resolution. The structure of the MreB protofilament is in remarkably good agreement with the model for F-actin, showing that the proteins assemble in identical orientations. The actin-like properties of MreB explain the finding that MreB forms large fibrous spirals under the cell membrane of rod-shaped cells, where they are involved in cell-shape determination. Thus, prokaryotes are now known to possess homologues both of tubulin, namely FtsZ, and of actin.