99 Teaching biological research using brown algae

Deserts are not thought of as biodiversity hotspots, but desert microbiotic crust communities represent a largely unknown community type rich in diversity of eukaryotic and prokaryotic taxa. These ecologically important communities have received much attention because of their role in nutrient cycling and soil stabilization in deserts, but they defy characterization by the traditional approach to assessing biodiversity by counting species. While genetically diverse, taxa characteristic of desert crusts are difficult to identify to the species level due to convergent evolution toward simple morphologies, phenotypic plasticity, or poor knowledge about particular lineages. Focusing on the green algae, we show that while biodiversity is difficult to measure in these communities, phylodiversity provides a surrogate measure that more accurately portrays the diversity of organisms, and one that is standardized across the variety of life histories, reproductive strategies and morphological variability that creates problems with species-counting measures. Bayesian phylogenetic inference uses MCMC simulation to generate phylogenies sampled in proportion to their Bayesian posterior probability. The length of a segment in any of these trees corresponds to the amount of change in the lineage, measured as the expected number of substitutions/nucleotide site. Comparisons of segment lengths corresponding to desert vs. other green algal lineages provides a means of addressing questions of relative genetic diversity, or phylodiversity, without complications arising from the difficulty of counting species. Our data illustrate the impact of desert green algae to overall knowledge of the green algal phylogenetic tree.     

98 Phylodiversity of green algae (chlorophyta) from desert microbiotic crusts

Deserts are not thought of as biodiversity hotspots, but desert microbiotic crust communities represent a largely unknown community type rich in diversity of eukaryotic and prokaryotic taxa. These ecologically important communities have received much attention because of their role in nutrient cycling and soil stabilization in deserts, but they defy characterization by the traditional approach to assessing biodiversity by counting species. While genetically diverse, taxa characteristic of desert crusts are difficult to identify to the species level due to convergent evolution toward simple morphologies, phenotypic plasticity, or poor knowledge about particular lineages. Focusing on the green algae, we show that while biodiversity is difficult to measure in these communities, phylodiversity provides a surrogate measure that more accurately portrays the diversity of organisms, and one that is standardized across the variety of life histories, reproductive strategies and morphological variability that creates problems with species‐counting measures. Bayesian phylogenetic inference uses MCMC simulation to generate phylogenies sampled in proportion to their Bayesian posterior probability. The length of a segment in any of these trees corresponds to the amount of change in the lineage, measured as the expected number of substitutions/nucleotide site. Comparisons of segment lengths corresponding to desert vs. other green algal lineages provides a means of addressing questions of relative genetic diversity, or phylodiversity, without complications arising from the difficulty of counting species. Our data illustrate the impact of desert green algae to overall knowledge of the green algal phylogenetic tree.     

Chlororespiration in Green Algae Isolated From Desert Crusts

Photosynthetic organisms enduring extreme temperatures, low water availability, or high light require photoprotective mechanisms to prevent sustained damage to photosynthetic machinery. Green microalgae living in desert crust communities of the south‐western US experience all these environmental stresses, yet photophysiological studies of green algae in the literature have focused on only a handful of common aquatic and marine species. We are examining the variation in green algal photoprotective mechanisms that is the result of natural selection acting independently in multiple lineages of highly diverse desert green algae (Chlorophyta) within the classes Chlorophyceae and Trebouxiophyceae. We have found that unusually extensive dark reduction of the plastoquinone pool is a prominent photophysiological feature among these desert algae; this reduction may be linked with enhanced chlororespiration. Recently, chlororespiration in higher plants has been linked through mutant analysis to control of the carotenoid synthetic pathway, heat stress, and starch metabolism among other pathways, though the function of chlororespiration remains controversial. Given that green algae and higher plants are monophyletic, analysis of potential chlororespiration in desert green algae may help decipher the evolution of the chlororespiratory process as well as its potential role in photoprotection in desert habitats.     

The xanthophyll cycle and NPQ in diverse desert and aquatic green algae

It has long been suspected that photoprotective mechanisms in green algae are similar to those in seed plants. However, exceptions have recently surfaced among aquatic and marine green algae in several taxonomic classes. Green algae are highly diverse genetically, falling into 13 named classes, and they are diverse ecologically, with many lineages including members from freshwater, marine, and terrestrial habitats. Genetically similar species living in dramatically different environments are potentially a rich source of information about variations in photoprotective function. Using aquatic and desert-derived species from three classes of green algae, we examined the induction of photoprotection under high light, exploring the relationship between nonphotochemical quenching and the xanthophyll cycle. In liquid culture, behavior of aquatic Entransia fimbriata (Klebsormidiophyceae) generally matched patterns observed in seed plants. Nonphotochemical quenching was lowest after overnight dark adaptation, increased with light intensity, and the extent of nonphotochemical quenching correlated with the extent of deepoxidation of xanthophyll cycle pigments. In contrast, overnight dark adaptation did not minimize nonphotochemical quenching in the other species studied: desert Klebsormidium sp. (Klebsormidiophyceae), desert and aquatic Cylindrocystis sp. (Zygnematophyceae), and desert Stichococcus sp. (Trebouxiophyceae). Instead, exposure to low light reduced nonphotochemical quenching below dark-adapted levels. De-epoxidation of xanthophyll cycle pigments paralleled light-induced changes in nonphotochemical quenching for species within Klebsormidiophyceae and Trebouxiophyceae, but not Zygnematophyceae. Inhibition of violaxanthin–zeaxanthin conversion by dithiothreitol reduced high-light-associated nonphotochemical quenching in all species (Zygnematophyceae the least), indicating that zeaxanthin can contribute to photoprotection as in seed plants but to different extents depending on taxon or lineage.     

Widespread desert affiliation of trebouxiophycean algae (Trebouxiophyceae,Chlorophyta) including discovery of three new desert genera

Unlike most other green algae, trebouxiophyceans are predominantly aerophytic and contain many symbiotic representatives. In recent years, a number of new terrestrial trebouxiophycean taxa were described from soils, tree bark, and lichens. The present phylogenetic study reveals three new lineages of free‐living trebouxiophyceans found in North American desert soil crusts and proposes new generic names to accommodate them: Desertella, Eremochloris, and Xerochlorella. This survey of desert isolates also led to discovery of representatives of seven existing genera of trebouxiophyceans. Two of these genera have never been reported to contain desert representatives and one was known previously only from aquatic habitats. Furthermore, we expand the known geographic range of the recently described genus Chloropyrula, heretofore only known from the Ural Mountains. We demonstrate that the diversity of trebouxiophyceans is still underestimated and poorly understood, and that most major trebouxiophycean lineages contain desert‐dwelling taxa.     

Photosynthetic recovery following desiccation of desert green algae (Chlorophyta) and their aquatic relatives

Recent molecular data suggest that desert green algae have evolved from freshwater ancestors at least 14 times in three major classes (Chlorophyceae, Trebouxiophyceae and Charophyceae), offering a unique opportunity to study the adaptation of photosynthetic organisms to life on land in a comparative phylogenetic framework. We examined the photorecovery of phylogenetically matched desert and aquatic algae after desiccation in darkness and under illumination. Desert algae survived desiccation for at least 4 weeks when dried in darkness, and recovered high levels of photosynthetic quantum yield within 1 h of rehydration in darkness. However, when 4 weeks of desiccation was accompanied by illumination, three of six desert taxa lost their ability to recover quantum yield during rehydration in the dark. Aquatic algae, in contrast, recovered very little during dark rehydration following even just 24 h of desiccation. Re-illuminating rehydrated algae produced a nearly complete recovery of quantum yield in all desert and two of five aquatic taxa. These contrasts provide physiological evidence that desert green algae possess mechanisms for photosynthetic recovery after desiccation distinct from those in aquatic relatives, corroborating molecular evidence that they are not happenstance, short-term visitors from aquatic environments. Photosensitivity during desiccation among desert algae further suggests that they may reside in protected microsites within crusts, and species specificity of photosensitivity suggests that disturbances physically disrupting crusts could lead to shifts or losses of taxonomic diversity within these habitats.     

CRYPTIC SPECIES OF SCENEDESMUS (CHLOROPHYTA) FROM DESERT SOIL COMMUNITIES OF WESTERN NORTH AMERICA1

Nine isolates of unicellular green algae were obtained from six geographically separate desert microbiotic crust communities in western North America. Microscopically, eight isolates strongly resembled unicellular forms of Scenedesmus obliquus (Turpin) Kützing. They are oval or crescent shaped, often flattened on one side, with knobby cell apices. SEM indicated a lack of wall ornamentation. Fine filaments connecting cells pole to pole were observed in some isolates, as previously documented in Scenedesmus (Dactylococcus) dissociatus and S. obliquus. The ninth isolate was spherical, without knobby apices or connections between cells, and was similar to unicellular forms that were originally classified as species of Chlorella (Scenedesmus vacuolatus and S. rubescens). None of the isolates formed coenobia in liquid culture. Phylogenetic analysis of the 18S rRNA gene placed all desert isolates in the genus Scenedesmus, separating them into two or three weakly resolved groups along with published sequences of other Scenedesmus isolates. Phylogenetic analyses of the internal transcribed spacer region revealed well‐supported lineages of desert algae that were unsupported with 18S data alone. The eight S. obliquus‐like desert strains formed two distinct clades that excluded the S. obliquus strains from geographically widespread nondesert habitats. The ninth strain was outside of the S. obliquus group, associated with S. raciborskii and S. pectinatus. These results demonstrate three lineages of Scenedesmus from desert soils and provide robust support for the presence of cryptic species in S. obliquus, a morphospecies that is said to have a cosmopolitan distribution. Three new species of Scenedesmus are described.     

Microbiotic Crusts and Ecosystem Processes

Microbiotic crusts are biological soil crusts composed of lichens, cyanobacteria, algae, mosses, and fungi. The biodiversity of these crusts is poorly understood; several cosmopolitan species dominate in most areas, but many species are confined to one or a few sites. Nitrogen fixation by organisms within the crust can be the dominant source of nitrogen input into many ecosystems, although rates of nitrogen input are limited by water availability, temperature, and nitrogen loss from the crust. Photosynthetic rates of the microbiotic crust can be 50% of those observed for higher plants, but the contribution of crusts to carbon cycling is not known. The microbiotic crust binds soil particles together, and this significantly increases soil surface stability and resistance to erosion. Greenhouse studies have found that crusts can enhance seed germination, seedling survivorship, and plant nutrient status, but further experiments are needed under field conditions. Crusts are extremely susceptible to surface disturbance and fire, and disruption of crusts can decrease soil fertility and stability resulting in lower nutrient availability for vascular plants and significant soil loss from the ecosystem.     

Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

相似文献   

荒漠地表生物土壤结皮形成与演替特征概述

土壤表面结皮是世界范围内干旱沙漠地区土壤表面广泛存在的自然现象,包括物理结皮和生物土壤结皮两大类型。其中,生物土壤结皮作为干旱沙漠地区特殊环境的产物,是由细菌、真菌、蓝绿藻、地衣和苔藓植物与土壤形成的有机复合体。它的形成使土壤表面在物理、化学和生物学特性上均明显不同于松散沙土,具有较强的抗风蚀功能和重要的生态效应,成为干旱沙漠地区植被演替的重要基础。随着形成生物土壤结皮的物种更替,维持结皮结构的主要胶结方式亦随之发生变化,即由胞外多糖的粘结作用逐渐转变为蓝藻和荒漠藻的藻丝体、地衣菌丝体以及苔藓植物假根的缠绕和捆绑作用,物种更替是结皮微结构和胶结方式转化的生物基础。生物土壤结皮的形成通常可以分为以下几个阶段:生物土壤结皮的早期阶段(土壤酶和土壤微生物),藻结皮阶段、地衣结皮阶段和苔藓结皮阶段。即随着土壤微生物在沙土表面的生长,随后出现丝状蓝藻和荒漠藻类植物,形成以藻类植物为主体的荒漠藻结皮;当土壤表面得到一定固定后,便开始出现地衣和苔藓植物,形成以地衣和苔藓植物为优势的生物结皮类型。其中,前一阶段的完成又为后一阶段的开始提供良好的环境条件。当环境条件适宜时,生物土壤结皮也可以不经历其中某个阶段而直接发育到更高级的阶段。     

ABRUPT DECELERATION OF MOLECULAR EVOLUTION LINKED TO THE ORIGIN OF ARBORESCENCE IN FERNS

Molecular rate heterogeneity, whereby rates of molecular evolution vary among groups of organisms, is a well‐documented phenomenon. Nonetheless, its causes are poorly understood. For animals, generation time is frequently cited because longer‐lived species tend to have slower rates of molecular evolution than their shorter‐lived counterparts. Although a similar pattern has been uncovered in flowering plants, using proxies such as growth form, the underlying process has remained elusive. Here, we find a deceleration of molecular evolutionary rate to be coupled with the origin of arborescence in ferns. Phylogenetic branch lengths within the “tree fern” clade are considerably shorter than those of closely related lineages, and our analyses demonstrate that this is due to a significant difference in molecular evolutionary rate. Reconstructions reveal that an abrupt rate deceleration coincided with the evolution of the long‐lived tree‐like habit at the base of the tree fern clade. This suggests that a generation time effect may well be ubiquitous across the green tree of life, and that the search for a responsible mechanism must focus on characteristics shared by all vascular plants. Discriminating among the possibilities will require contributions from various biological disciplines, but will be necessary for a full appreciation of molecular evolution.     

Occurrence of matK in a trnK group II intron in charophyte green algae and phylogeny of the Characeae

A group II intron containing the matK gene, which encodes a splicing-associated maturase, was found in the trnK (lysine tRNA) exon in the chloroplast genome of the six extant genera of green algae in the family Characeae, which among green algae are the sister group to embryophytes (land plants). The characean trnK intron (～2.5 kilobases [kb]) and matK ORF (～1.5 kb) are comparable in size to the intron and ORF of land plants, in which they are similarly found inserted in the trnK exon. Domain X, a sequence of conserved amino acid residues within matK, occurs in the Characeae. Phylogenetic analysis using maximum likelihood (GTR + I + gamma likelihood model) and parsimony (branch and bound search) yielded one tree with high bootstrap support for all branches. The matK tree was congruent with the rbcL tree for the same taxa. The number and proportion of informative sites was higher in matK (501, 31% of matK sequence) compared to rbcL (122, 10%). Characeae branch lengths were on average more than five times longer for matK compared to rbcL and provided better resolution within the Characeae. These findings along with recent genomic analyses demonstrate that the intron and matK invaded the chloroplast genome of green algae prior to the evolution of land plants.     

Phylogenetic tree of vascular plants reveals the origins of aquatic angiosperms

Although aquatic plants are discussed as a unified biological group, they are phylogenetically well dispersed across the angiosperms. In this study, we annotated the aquatic taxa on the tree of vascular plants, and extracted the topology of these aquatic lineages to construct the tree of aquatic angiosperms. We also reconstructed the ancestral areas of aquatic families. We found that aquatic angiosperms could be divided into two different categories: the four aquatic orders and the aquatic taxa in terrestrial orders. Aquatic lineages evolved early in the radiation of angiosperms, both in the orders Nymphaeales and Ceratophyllales and among basal monocots (Acorales and Alismatales). These aquatic orders do not have any extant terrestrial relatives. They originated from aquatic habitats during the Early Cretaceous. Asia would have been one of the centers for early diversification of aquatic angiosperms. The aquatic families within terrestrial orders may originate from other areas besides Asia, such as America or Australia. The lineages leading to extant angiosperms diversified early in underexploited freshwater habitats. The four extant aquatic orders were relicts of an early radiation of angiosperm in aquatic environments. Their extinct ancestors might be aquatic early angiosperms.     

The GapA/B gene duplication marks the origin of Streptophyta (charophytes and land plants)

Independent evidence from morphological, ultrastructural, biochemical, and molecular data have shown that land plants originated from charophycean green algae. However, the branching order within charophytes is still unresolved, and contradictory phylogenies about, for example,the position of the unicellular green alga Mesostigma viride are difficult to reconcile. A comparison of nuclear-encoded Calvin cycle glyceraldehyde-3-phosphate dehydrogenases (GAPDH) indicates that a crucial duplication of the GapA gene occurred early in land plant evolution. The duplicate called GapB acquired a characteristic carboxy-terminal extension (CTE) from the general regulator of the Calvin cycle CP12. This CTE is responsible for thioredoxin-dependent light/dark regulation. In this work, we established GapA, GapB, and CP12 sequences from bryophytes, all orders of charophyte as well as chlorophyte green algae, and the glaucophyte Cyanophora paradoxa. Comprehensive phylogenetic analyses of all available plastid GAPDH sequences suggest that glaucophytes and green plants are sister lineages and support a positioning of Mesostigma basal to all charophycean algae. The exclusive presence of GapB in terrestrial plants, charophytes, and Mesostigma dates the GapA/B gene duplication to the common ancestor of Streptophyta. The conspicuously high degree of GapB sequence conservation suggests an important metabolic role of the newly gained regulatory function. Because the GapB-mediated protein aggregation most likely ensures the complete blockage of the Calvin cycle at night, we propose that this mechanism is also crucial for efficient starch mobilization. This innovation may be one prerequisite for the development of storage tissues in land plants.     

A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies

Background  

The Viridiplantae comprise two major phyla: the Streptophyta, containing the charophycean green algae and all land plants, and the Chlorophyta, containing the remaining green algae. Despite recent progress in unravelling phylogenetic relationships among major green plant lineages, problematic nodes still remain in the green tree of life. One of the major issues concerns the scaly biflagellate Mesostigma viride, which is either regarded as representing the earliest divergence of the Streptophyta or a separate lineage that diverged before the Chlorophyta and Streptophyta. Phylogenies based on chloroplast and mitochondrial genomes support the latter view. Because some green plant lineages are not represented in these phylogenies, sparse taxon sampling has been suspected to yield misleading topologies. Here, we describe the complete chloroplast DNA (cpDNA) sequence of the early-diverging charophycean alga Chlorokybus atmophyticus and present chloroplast genome-based phylogenies with an expanded taxon sampling.     

A molecular timeline for the origin of photosynthetic eukaryotes

The appearance of photosynthetic eukaryotes (algae and plants) dramatically altered the Earth's ecosystem, making possible all vertebrate life on land, including humans. Dating algal origin is, however, frustrated by a meager fossil record. We generated a plastid multi-gene phylogeny with Bayesian inference and then used maximum likelihood molecular clock methods to estimate algal divergence times. The plastid tree was used as a surrogate for algal host evolution because of recent phylogenetic evidence supporting the vertical ancestry of the plastid in the red, green, and glaucophyte algae. Nodes in the plastid tree were constrained with six reliable fossil dates and a maximum age of 3,500 MYA based on the earliest known eubacterial fossil. Our analyses support an ancient (late Paleoproterozoic) origin of photosynthetic eukaryotes with the primary endosymbiosis that gave rise to the first alga having occurred after the split of the Plantae (i.e., red, green, and glaucophyte algae plus land plants) from the opisthokonts sometime before 1,558 MYA. The split of the red and green algae is calculated to have occurred about 1,500 MYA, and the putative single red algal secondary endosymbiosis that gave rise to the plastid in the cryptophyte, haptophyte, and stramenopile algae (chromists) occurred about 1,300 MYA. These dates, which are consistent with fossil evidence for putative marine algae (i.e., acritarchs) from the early Mesoproterozoic (1,500 MYA) and with a major eukaryotic diversification in the very late Mesoproterozoic and Neoproterozoic, provide a molecular timeline for understanding algal evolution.     

Transit peptide diversity and divergence: A global analysis of plastid targeting signals

Proteins are targeted to plastids by N-terminal transit peptides, which are recognized by protein import complexes in the organelle membranes. Historically, transit peptide properties have been defined from vascular plant sequences, but recent large-scale genome sequencing from the many plastid-containing lineages across the tree of life has provided a much broader representation of targeted proteins. This includes the three lineages containing primary plastids (plants and green algae, rhodophytes and glaucophytes) and also the seven major lineages that contain secondary plastids, "secondhand" plastids derived through eukaryotic endosymbiosis. Despite this extensive spread of plastids throughout Eukaryota, an N-terminal transit peptide has been maintained as an essential plastid-targeting motif. This article provides the first global comparison of transit peptide composition and summarizes conservation of some features, the loss of an ancestral motif from the green lineages including plants, and modifications to transit peptides that have occurred in secondary and even tertiary plastids.     

生物土壤结皮对荒漠土壤种子库和种子萌发的影响

研究了腾格里沙漠东南缘在不同自然条件（风、温度、水分）下,人工固沙植被区（24龄、41龄、50龄）和相邻天然植被区的两种生物土壤结皮对荒漠土壤种子库和种子萌发的影响。结果表明,荒漠土壤种子库在苔藓结皮上的储量显著高于藻类结皮。随着生物土壤结皮的发育,种子萌发量在苔藓结皮上增加,在藻类结皮上减少。生物土壤结皮层的含水量对种子萌发有显著的影响（p〈0.05）,植物种子在湿润处理的生物土壤结皮上的萌发量高于干燥处理的生物土壤结皮上的种子萌发量。生物土壤结皮表层温度和亚表层温度对荒漠植物种子萌发无显著影响（p〉0.05）,但总体而言,对于苔藓结皮,植物种子在较高温度下的萌发量略高于在较低温度下的萌发量,而对于藻类结皮,植物种子在较低温度下的萌发量略高。     

Alternative oxidase (AOX) genes of African trypanosomes: phylogeny and evolution of AOX and plastid terminal oxidase families

To clarify evolution and phylogenetic relationships of trypanosome alternative oxidase (AOX) molecules, AOX genes (cDNAs) of the African trypanosomes, Trypanosoma congolense and Trypanosoma evansi, were cloned by PCR. Both AOXs possess conserved consensus motifs (-E-, -EXXH-). The putative amino acid sequence of the AOX of T. evansi was exactly the same as that of T. brucei. A protein phylogeny of trypanosome AOXs revealed that three genetically and pathogenically distinct strains of T. congolense are closely related to each other. When all known AOX sequences collected from current databases were analyzed, the common ancestor of these three Trypanosoma species shared a sister-group position to T. brucei/T. evansi. Monophyly of Trypanosoma spp. was clearly supported (100% bootstrap value) with Trypanosoma vivax placed at the most basal position of the Trypanosoma clade. Monophyly of other eukaryotic lineages, terrestrial plants + red algae, Metazoa, diatoms, Alveolata, oomycetes, green algae, and Fungi, was reconstructed in the best AOX tree obtained from maximum likelihood analysis, although some of these clades were not strongly supported. The terrestrial plants + red algae clade showed the closest affinity with an alpha-proteobacterium, Novosphingobium aromaticivorans, and the common ancestor of these lineages, was separated from other eukaryotes. Although the root of the AOX subtree was not clearly determined, subsequent phylogenetic analysis of the composite tree for AOX and plastid terminal oxidase (PTOX) demonstrated that PTOX and related cyanobacterial sequences are of a monophyletic origin and their common ancestor is linked to AOX sequences.     

The Transition From Algae to Embryophytes: Chloroplast Phylogenomic Evidence (II)

The transition of plant life from aquatic algae to land plants was one of the major events in the history of life. However, in hypothesizing the evolutionary path of the transition, limited shared phenotypic characters in aquatic algae and land plants (embryophytes) have been a major hinderance. Chloroplast genomes contain characters useful in tracing evolutionary histories. Embryophyte chloroplast genomes are distinguished from algal cpDNAs by the presence of over 20 group II introns and three ribosomal protein operons (rpl23, clpP and 3?rps12 operons). These phylogenomic features indicate a phylogenetic relationship of charophytes and embryophytes. In addition to these operons and introns, the evolution of rRNA and psbB operon evolution of streptophyte lineages will be incorporated with major biological phenotypic features to produce a phylogenetic tree. Basal embryophytes, the antithetic hypothesis, monophyly of embryophytes, and paraphyly of charophytes will be discussed. Strepotophytes are classified into three major groups (basal streptophytes, mid‐divergent streptophytes and late divergent charophytes‐embryophytes).