Paleobiological Perspectives on Early Eukaryotic Evolution

Eukaryotic organisms radiated in Proterozoic oceans with oxygenated surface waters, but, commonly, anoxia at depth. Exceptionally preserved fossils of red algae favor crown group emergence more than 1200 million years ago, but older (up to 1600–1800 million years) microfossils could record stem group eukaryotes. Major eukaryotic diversification ∼800 million years ago is documented by the increase in the taxonomic richness of complex, organic-walled microfossils, including simple coenocytic and multicellular forms, as well as widespread tests comparable to those of extant testate amoebae and simple foraminiferans and diverse scales comparable to organic and siliceous scales formed today by protists in several clades. Mid-Neoproterozoic establishment or expansion of eukaryophagy provides a possible mechanism for accelerating eukaryotic diversification long after the origin of the domain. Protists continued to diversify along with animals in the more pervasively oxygenated oceans of the Phanerozoic Eon.Eukaryotic organisms have a long evolutionary history, recorded, in part, by conventional and molecular fossils. For the Phanerozoic Eon (the past 542 million years), eukaryotic evolution is richly documented by the skeletons (and, occasionally, nonskeletal remains) of animals, as well as the leaves, stems, roots, and reproductive organs of land plants. Phylogenetic logic, however, tells us that eukaryotes must have a deeper history, one that began long before the first plant and animal fossils formed. To what extent does the geological record preserve aspects of deep eukaryotic history, and can the chemistry of ancient sedimentary rocks elucidate the environmental conditions under which the eukaryotic cell took shape?     

微生物除草剂的研究进展与展望

综述了国内外微生物除草剂的研究进展,介绍5种已经商品化的微生物除草剂和包括真菌、根际细菌、病毒、放线菌4种具有除草潜能的微生物类型的除草剂,并对我国微生物除草剂的研究开发提出了建议。     

New Perspectives on Microbial Community Distortion after Whole-Genome Amplification

Whole-genome amplification (WGA) has become an important tool to explore the genomic information of microorganisms in an environmental sample with limited biomass, however potential selective biases during the amplification processes are poorly understood. Here, we describe the effects of WGA on 31 different microbial communities from five biotopes that also included low-biomass samples from drinking water and groundwater. Our findings provide evidence that microbiome segregation by biotope was possible despite WGA treatment. Nevertheless, samples from different biotopes revealed different levels of distortion, with genomic GC content significantly correlated with WGA perturbation. Certain phylogenetic clades revealed a homogenous trend across various sample types, for instance Alpha- and Betaproteobacteria showed a decrease in their abundance after WGA treatment. On the other hand, Enterobacteriaceae, an important biomarker group for fecal contamination in groundwater and drinking water, were strongly affected by WGA treatment without a predictable pattern. These novel results describe the impact of WGA on low-biomass samples and may highlight issues to be aware of when designing future metagenomic studies that necessitate preceding WGA treatment.     

Two Perspectives on the Evolution of the Tetrapod Limb

SYNOPSIS. The evolution of the tetrapod limb is examined fromtwo perspectives: structural and functional. Rosen et al. (1981)argued that lungfishes are the sister group of tetrapods, withlimb characteristics comprising an important subset of theirevidence. A re-analysis of the limb characters advocated byRosen et al. does not support their contention, but insteadsuggests that rhipidistian fishes of the family Osteolepidaeare the closest relatives of the tetrapods. In order to understandthe probable selective pressures leading to evolution of thetetrapod limb, a functional analysis of the fins of antennariidanglerfishes was performed. Antennariids use their limb-likefins to traverse underwater substrates. The analysis revealsa large number of functional and morphological convergencesbetween antennariid fins and tetrapod limbs. It is suggestedthat tetrapod limbs were evolved for underwater transport ratherthan for locomotion on dry land.     

Early Development of Soil Microbial Communities on Rehabilitated Quarries

The ecological development of soil microbial communities was studied in terms of microbial composition and structure at different rehabilitated phases on three quarries, namely Turret Hill Quarry (TH), Lam Tei Quarry (LT), and Shek O Quarry (SO), in Hong Kong. Using individual fatty acid methylesters (FAMEs) as biomarkers, Gram^? bacteria dominated at all sites, in which cy19:0 represented more than 15% of the total extracted FAMEs in all soils tested. Redundancy analysis showed that the abundance of Gram^? bacteria and Gram⁺ bacteria correlated significantly with woody species richness, native species richness, organic C, total N, and extractable NO₃‐N. Fungi (18:1w9c and 18:2w6) and arbuscular mycorrhizal (AM) fungi (16:1w5c) decreased in abundance with increasing age in SO and LT, which were positively correlated with grass coverage, soil pH, extractable NH₄‐N, and extractable P. Our study suggested that soil aeration and C availability in soils played a dominant role driving the changes in the composition and structure of Gram^? bacteria and Gram⁺ bacteria communities. Available P was the limiting factor for regulating the fungal and AM fungal communities on our local quarries.     

Early Evolution of Immunoglobulin Genes

Considerable progress has been made in the characterizationof immunoglobulin genes from several lower vertebrate taxa.Isolation and identification of immunoglobulin genes in phylogeneticallyprimitive species is based predominantly on heterologous crosshybridization.The unit, clustered organization of heavy chain segmental elementsobserved in the germline of the horned shark (Hinds and Litman,1986) has also been found in another elasmobranch. Studies todetermine whether the clustered organization is universal throughoutthe entire cartilaginous fish assemblage are ongoing. In contrast,the ray-finned (bony)fishes appear to possess a mammalian-typeheavy chain gene organization. Additionally, immunoglobulingenes are being characterized in two relict fish species whoseexact systematic relationships are unknown. Isolation of putativeimmunoglobulin genes from the phylogenetically- ancient hagfishis being attempted using a PCR-based approach. Other ongoingor future research efforts involve characterization of lowervertebrate light chain genes, heavy chain isotype evolution,and the divergence of the immunoglobulins and T-cell antigenreceptors     

微生物酶的分子改性和人工进化的研究进展

运用分子生物学技术对微生物来源的酶进行分子改性和人工进化在过去几年中取得了令人瞩目的进展。本文综述了用于酶分子改性和人工进化的主要分子生物学方法,如易错PCR技术、DNA体外随机拼接技术等及其在酶的分子进化和改性中应用成就。     

Tracing the Early Emergence of Microbial Sulfur Metabolisms

Abstract

Hydrogen sulfide (nH₂S) and sulfur oxide (SO _n ; n?=?1, 2, 3) gases in early Earth’s globally anoxic atmosphere were subjected to gas-phase chemical transformations by UV light. A principal photolysis pathway at that time produced elemental sulfur aerosols with mass-independently fractionated (MIF) isotopic values carrying variable minor isotope (³³S, ³⁶S) compositions. These rained into the sulfate-deficient Archean (ca. 3.85–2.5 Ga) oceans to react with [Fe²⁺]_aq and form sedimentary sulfides. The MIF-bearing sulfides were incorporated into Archean sediments, including banded iron formations (BIF). Such aerosols may also have fueled microbial sulfur metabolisms, and thus are traceable by the MIF sulfur isotopes. Yet, data show that before ～3.5 Ga mass-dependent³⁴S/³²S values in Early Archean sediments tend to fall within a narrow (±0.1%) range even as they carry mass-independent values. By about 3.5 Ga, ³⁴S/³²S values show much greater changes (>1%) in range congruent with microbial metabolic processing. Here, we trace probable pathways of elemental sulfur aerosols into Archean sediments, and couple our study with analysis of the evolutionary relationships of enzymes involved in sulfur metabolism to explain the observed trends. Our model explains why elemental sulfur aerosols were apparently not utilized by the Eoarchean (pre-3.65 Ga) biosphere even though an immediate precursor to the required enzyme may have already been present.

• Highlights

• Evolution of microbial sulfur metabolisms is tracked by multiple sulfur isotopes

• Alkaline hydrothermal vents were an abode for early microbial life

• Sulfite detoxification prompted anaerobic respiration

• Reversal of respiratory electron transport chain (ETC) stimulated photothiotrophy

• Surplus e- acceptors permitted the emergence of elemental sulfur reduction