Phylogenetic analysis of cultivation‐resistant terrestrial cyanobacteria with massive sheaths (Stigonema spp. and Petalonema alatum,Nostocales, Cyanobacteria) using single‐cell and filament sequencing of environmental samples

Molecular assessment of a large portion of traditional cyanobacterial taxa has been hindered by the failure to isolate and grow them in culture. In this study, we developed an optimized protocol for single cell/filament isolation and 16S rRNA gene sequencing of terrestrial cyanobacteria with large mucilaginous sheaths, and applied it to determine the phylogenetic position of typical members of the genera Petalonema and Stigonema. A methodology based on a glass‐capillary isolation technique and a semi‐nested PCR protocol enabled reliable sequencing of the 16S rRNA gene from all samples analyzed. Ten samples covering seven species of Stigonema from Europe, North and Central America, and Hawaii, and the type species of Petalonema from Slovakia were sequenced. Contrary to some previous studies, which proposed a relationship with heteropolar nostocalean cyanobacteria, Petalonema appeared to belong to the family Scytonemataceae. Analysis of Stigonema specimens recovered a unique coherent phylogenetic cluster, substantially broadening our knowledge of the molecular diversity within this genus. Neither the uni‐ to biseriate species nor the multiseriate species formed monophyletic subclusters within the genus. Typical multiseriate species of Stigonema clustered in a phylogenetic branch derived from uni‐ to biseriate S. ocellatum Thuret ex Bornet & Flahault in our analysis, suggesting that species with more complex thalli may have evolved from the more simple ones. We propose the technique tested in this study as a promising tool for a future revision of the molecular taxonomy in cyanobacteria.     

Morphological,biochemical and phylogenetic assessments of water‐bloom‐forming tropical morphospecies of Microcystis (Chroococcales,Cyanobacteria)

Previous polyphasic analyses of five morphospecies of the water‐bloom‐forming cyanobacterial genus Microcystis, Microcystis aeruginosa (Kützing) Lemmermann (=Microcystis aeruginosa (Kützing) Kützing), Microcystis ichthyoblabe Kützing, Microcystis novacekii (Komárek) Compère, Microcystis viridis (A. Braun) Lemmermann, and Microcystis wesenbergii (Komárek) Komárek in Kondratieva, have shown them to be conspecific and they have been proposed to be included under the binomial Microcystis aeruginosa (Kützing) Lemmermann. However, several morphospecies from tropical regions, such as Microcystis bengalensis Banerji, Microcystis panniformis Komárek, Komárková‐Legnerová, Sant'anna, Azevedo & Senna, Microcystis protocystis Crow, Microcystis pseudofilamentosa Crow, Microcystis ramosa Bharadwaya, and Microcystis robusta (Clark) Nygaard, have never been analyzed biochemically or phylogenetically; consequently, their taxonomic status is uncertain. To resolve this issue, we collected 57 strains of Microcystis from Vietnam for taxonomic analysis using a polyphasic approach. Strains were assigned to the six tropical morphospecies listed above or to four morphospecies with cosmopolitan distributions (M. aeruginosa, M. ichthyoblabe, M. novacekii, and M. wesenbergii). Several strains produced colony variants in different culture media; some of these variants had forms that overlapped with those of other morphospecies. Cell diameters varied widely between strains (2.6–9.3 µm) and were unrelated to morphospecies discrimination criteria. Strains of the 10 morphospecies examined had similar fatty acid compositions and closely similar 16S rRNA gene sequences (>99.2% similar). Phylogenetic analyses using 16S rRNA gene and 16S–23S internal transcribed spacer sequences did not identify any clear separations corresponding to morphospecies concepts or microcystin‐producing abilities. Thus, the six tropical morphospecies (M. bengalensis, M. panniformis, M. protocystis, M. pseudofilamentosa, M. ramosa, and M. robusta) are not natural taxonomic units within the genus Microcystis and should be included under M. aeruginosa.     

Morphological and molecular characterization within 26 strains of the genus Cylindrospermum (Nostocaceae,Cyanobacteria), with descriptions of three new species

Twenty‐six strains morphologically identified as Cylindrospermum as well as the closely related taxon Cronbergia siamensis were examined microscopically as well as phylogenetically using sequence data for the 16S rRNA gene and the 16S‐23S internal transcribed spacer (ITS) region. Phylogenetic analysis of the 16S rRNA revealed three distinct clades. The clade we designate as Cylindrospermum sensu stricto contained all five of the foundational species, C. maius, C. stagnale, C. licheniforme, C. muscicola, and C. catenatum. In addition to these taxa, three species new to science in this clade were described: C. badium, C. moravicum, and C. pellucidum. Our evidence indicated that Cronbergia is a later synonym of Cylindrospermum. The phylogenetic position of Cylindrospermum within the Nostocaceae was not clearly resolved in our analyses. Cylindrospermum is unusual among cyanobacterial genera in that the morphological diversity appears to be more evident than sequence divergence. Taxa were clearly separable using morphology, but had very high percent similarity among ribosomal sequences. Given the high diversity we noted in this study, we conclude that there is likely much more diversity remaining to be described in this genus.     

Macrochaete gen. nov. (Nostocales,Cyanobacteria), a taxon morphologically and molecularly distinct from Calothrix

Historically, the genus Calothrix included all noncolonial, tapered, heterocytous filaments within the cyanobacteria. However, recent molecular phylogenies show that “Calothrix” defined in this sense represents five distinct clades. The type species of Calothrix is marine, with solitary basal heterocytes, no akinetes, and distal ends tapering abruptly into short hairs. We examined the morphology and phylogeny of 45 tapering cyanobacteria in the Rivulariaceae, including freshwater and marine representatives of both Calothrix (35 strains) and its sister taxon Rivularia (10 strains). The marine Calothrix fall into two lineages, but we lack the generitype and so cannot identify the clade corresponding to the type species. The freshwater and soil Calothrix fall into the C. parietina clade and are characterized by having a basal heterocyte, no akinetes, and gradual tapering—but not into a long hyaline hair. Macrochaete gen. nov. is a freshwater taxon sister to the Calothrix lineages but clearly separated from Rivularia. The species in this genus differ morphologically from Calothrix by their ability to produce two heteromorphic basal heterocytes and specific secondary structures of the 16S–23S ITS. An additional feature present in most species is the presence of a distal, long hyaline hair, but this character has incomplete penetrance due to its expression only under specific environmental conditions (low phosphate), and in one species appears to be lost. We recognize three species: M. psychrophila (type species) from cold environments (high mountains, Antarctica), M. santannae from wet walls of subtropical South America, and M. lichenoides, a phycobiont of lichens from Europe.     

Cyanomargarita gen. nov. (Nostocales,Cyanobacteria): convergent evolution resulting in a cryptic genus

Two populations of Rivularia‐like cyanobacteria were isolated from ecologically distinct and biogeographically distant sites. One population was from an unpolluted stream in the Kola Peninsula of Russia, whereas the other was from a wet wall in the Grand Staircase‐Escalante National Monument, a desert park‐land in Utah. Though both were virtually indistinguishable from Rivularia in field and cultured material, they were both phylogenetically distant from Rivularia and the Rivulariaceae based on both 16S rRNA and rbcLX phylogenies. We here name the new cryptic genus Cyanomargarita gen. nov., with type species C. melechinii sp. nov., and additional species C. calcarea sp. nov. We also name a new family for these taxa, the Cyanomargaritaceae.     

Characterization of halotolerant rhizobia isolated from root nodules of Canavalia rosea from seaside areas

Twelve nodule isolates from Canavalia rosea, an indigenous leguminous halophyte growing in the seaside areas of southern Taiwan, were effective symbionts for the original host and able to grow at NaCl concentrations up to 3-3.5% (w/v). The taxonomy of these isolates was investigated using a polyphasic approach, including phenotypic characteristics, banding patterns of total proteins from sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), genomic fingerprint patterns from random amplified polymorphic DNA (RAPD) analysis, pulsed-field gel electrophoresis (PFGE) analysis, amplified 16S rDNA restriction analysis (ARDRA), 16S rRNA gene sequencing, and nifH gene sequencing. Based on the SDS-PAGE, RAPD, PFGE and ARDRA results, the 12 isolates are highly diverse. The 16S rRNA and nifH gene sequences were determined for isolates with distinct ARDRA patterns and compared with other members of the rhizobial species. We propose these isolates should be classified into the genus Sinorhizobium and distinguished from the current species of this genus.     

基于线粒体12S和16S rRNA基因部分序列探讨蚱科12种的系统发育关系

用ABI377自动测序仪测定了蚱科5属11个种的12s和16S rRNA基因部分序列,并从GenBank获得1属1种的同源序列;用Clustal X1．81比较其同源性,用Mega2．1计算序列变异性和遗传距离。在获得的736bp序列中,A T含量为71．2％～77．5％,平均为73．9％;G C含量为22．5％～28．8％,平均为26．1％。经Clustal X1．81软件比对,共得到755个位点,其中简约信息位点185个。以Cylindraustralia kochii为外群,构建NJ、MP和ML分子系统树,结果表明：(1)蚱属并非一个单系群,而是一个并系群;(2)环江柯蚱Coptltettix huanjiangensis和贡山柯蚱C.gongshanensis为同一个种,即贡山柯蚱,而环江柯蚱是贡山柯蚱的同物异名。     

Novel diversity within Roseofilum (Desertifilaceae,Cyanobacteria) from marine benthic mats with description of four new species

Benthic cyanobacterial mats (BCMs) are natural phenomena in marine environments. Reports of BCMs occurring across coastal marine environments have increased, partly driven by nutrient loading and climate change; thus, there is a need to understand the diversity involved in the proliferations and potential toxicity of the BCMs. Furthermore, marine cyanobacterial mats are observed growing on and affecting the health of corals with one specific cyanobacterial genus, Roseofilum, dominating the microbial mats associated with black band disease (BBD), a destructive polymicrobial disease that affects corals. To explore the diversity of Roseofilum, cyanobacterial mats from various marine habitats were sampled, and individual isolates were identified based on morphology, 16S rRNA gene phylogenies, 16S–23S ITS rRNA region sequence dissimilarities, and phylogenomics. Four novel species of Roseofilum were isolated from benthic marine mats, three from the coasts of Florida, United States (R. capinflatum sp. nov., R. casamattae sp. nov., and R. acuticapitatum sp. nov.) and one from the coast of France (R. halophilum sp. nov.). Our analyses revealed that Roseofilum associated with coral BBD and those not associated with corals but rather from coastal benthic mats are systematically distinct based on both phylogenetic and phylogenomic analyses. Enzyme-linked immunosorbent assay (ELISA) and LC–MS data indicated that microcystin production was found in one of the four species.     

Odorella benthonica gen. & sp. nov. (Pleurocapsales,Cyanobacteria): an odor and prolific toxin producer isolated from a California aqueduct

Pleurocapsales are one of the least understood groups of cyanobacteria in terms of molecular systematics and biochemistry. Considering the high number of cryptic taxa within the Synechococcales and Oscillatoriales, it is likely that such taxa also occur in the Pleurocapsales. The new genus described in our research is the first known pleurocapsalean cryptic taxon. It produces off‐flavor and a large number of bioactive metabolites (n = 38) some of which can be toxic including four known microcystins. Using a polyphasic approach, we propose the establishment of the genus Odorella with the new species O. benthonica from material originally isolated from the California Aqueduct near Los Angeles.     

A freshwater analog for the production of Epiphyton‐like microfossils

Calcified microbial microfossils—often interpreted as cyanobacteria—were important components of Precambrian and Paleozoic limestones, but their paucity in modern marine environments complicates our ability to make conclusive interpretations about their taxonomic affinity and geologic significance. Freshwater spring‐associated limestones (e.g., travertine and tufa) serve as terrestrial analogs to investigate mineralization in and around aquatic biofilms on observable timescales. We document the diagenesis of calcite fabrics associated with the freshwater algae Oocardium stratum, an epiphytic colonial green algae (desmid) known for producing stalks of extracellular polymeric substances (EPS) and passively producing a bifurcating tubular calcite monocrystal. Bifurcating EPS stalks produced by Oocardium colonies can become calcified and preserved in ancient carbonate deposits. Calcified micritic EPS stalks have a filamentous morphology, show evidence of branching, and maintain uniformity in diameter thickness throughout the mm‐scale colony, much like the enigmatic calcimicrobe Epiphyton. We provide a mechanism by which calcification associated with a colonial semispherical micro‐organism produces microfossils that deceptively resemble filamentous forms. These findings have implications for the use of morphological traits when assigning taxonomic affinities to extinct microfossil groups and highlight the utility of calcifying freshwater modern environments to investigate microbial taphonomy.     

A comparison of DNA- and RNA-based clone libraries from the same marine bacterioplankton community

Clones from the same marine bacterioplankton community were sequenced, 100 clones based on DNA (16S rRNA genes) and 100 clones based on RNA (16S rRNA). This bacterioplankton community was dominated by alpha-Proteobacteria in terms of repetitive DNA clones (52%), but gamma-Proteobacteria dominated in terms of repetitive RNA clones (44%). The combined analysis led to a characterization of phylotypes otherwise uncharacterized if only the DNA or RNA libraries would have been analyzed alone. Of the DNA clones, 25.5% were found only in this library and no close relatives were detected in the RNA library. For clones from the RNA library, 21.5% of RNA clones did not indicate close relatives in the DNA library. Based on the comparisons between DNA and RNA libraries, our data indicate that the characterization of the bacterial community based on RNA has the potential to characterize distinct phylotypes from the marine environment, which remain undetected on the DNA level.     

DNA‐based phylogeny of the marine genus Heterodrilus (Annelida,Clitellata, Naididae)

Heterodrilus is a group of marine Naididae, common worldwide in subtropical and tropical areas, and unique among the oligochaetes by their tridentate chaetae. The phylogenetic relationships within the group are assessed from the nuclear 18S rDNA gene, and the mitochondrial cytochrome c oxidase subunit I (COI) and 16S rDNA genes. Sequence data were obtained from 16 Heterodrilus species and 13 out‐group taxa; 48 sequences are new for this study. The data were analysed by Bayesian inference. Monophyly of the genus is corroborated by the resulting tree, with Heterodrilus ersei (a taxon representing a small group of species with aberrant male genitalia) proposed to be outside all other sampled species. Although earlier regarded as a member of the subfamily Rhyacodrilinae, both molecular and morphological data seem to support that Heterodrilus is closely related to Phallodrilinae. However, the results are not conclusive as to whether the genus is the sister group of, or a group nested inside, or separate from this latter subfamily. The studied sample of species suggests at least two major clades in Heterodrilus with different geographical distributions, in one of the clades, most species are from the Indo‐West Pacific Ocean, while in the other, the majority are from the Western Atlantic Ocean. Morphological characters traditionally used in Heterodrilus taxonomy are optimized on the phylogenetic tree, revealing a high degree of homoplasy.     

Complex estimates of evolutionary relationships in Tarentola mauritanica (Reptilia: Gekkonidae) derived from mitochondrial DNA sequences

Mitochondrial DNA (12S rRNA, 16S rRNA) sequences were analysed within Tarentola mauritanica and other selected species of Tarentola. Several highly genetically distinct lineages occur in North Africa, revealing phylogroups in southern and central Morocco, northern Morocco, Algeria, Tunisia, and Libya. A single haplotype characterizes populations across Spain, Portugal, Italy, Menorca, Crete, and Tunisia raising the possibility of an anthropogenic introduction followed by rapid population expansion throughout southern Europe. T. mauritanica is paraphyletic with respect to T. angustimentalis, a Canary islands endemic. The high genetic diversity observed across North Africa suggests T. mauritanica may represent a species complex.     

A bridge too far in naming species: a total evidence approach does not support recognition of four species in Desertifilum (Cyanobacteria)

A population of Desertifilum (Cyanobacteria, Oscillatoriales) from an oligotrophic desertic biotope was isolated and characterized using a polyphasic approach including molecular, morphological, and ecological information. The population was initially assumed to be a new species based on ecological and biogeographic separation from other existing species, however, phylogenetic analyses based on sequences of the 16S rRNA gene and 16S–23S ITS region, placed this strain clearly within the type species, Desertifilum tharense. Comparative analysis of morphology, 16S rRNA gene similarity, 16S–23S ITS secondary structure, and percent dissimilarity of the ITS regions for all characterized strains supports placing the six Desertifilum strains (designated as PD2001/TDC17, UAM‐C/S02, CHAB7200, NapGTcm17, IPPAS B‐1220, and PMC 872.14) into D. tharense. The recognition of Desertifilum salkalinema and Desertifilum dzianense is not supported, although our analysis does support continued recognition of Desertifilum fontinale. Pragmatic criteria for recognition of closely related species are proposed based on this study and others, and more rigorous review of future taxonomic papers is recommended.     

Mixotrophy and loss of phototrophy among geographic isolates of freshwater Esoptrodinium/Bernardinium sp. (Dinophyceae)

The genus Esoptrodinium Javornický consists of freshwater, athecate dinoflagellates with an incomplete cingulum. Strains isolated thus far feed on microalgae and most possess obvious pigmented chloroplasts, suggesting mixotrophy. However, some geographic isolates lack obvious pigmented chloroplasts. The purpose of this study was to comparatively examine this difference and the associated potential for mixotrophy among different isolates of Esoptrodinium. All isolates phagocytized prey cells through an unusual hatch‐like peduncle located on the ventral episome, and were capable of ingesting various protist taxa. All Esoptrodinium isolates required both food and light to grow. However, only the tested strain with visible pigmented chloroplasts benefited from light in terms of increased biomass (phototrophy). Isolates lacking obvious chloroplasts received no biomass benefit from light, but nevertheless required light for sustained growth (i.e., photoobligate, but not phototrophic). Isolates with visible chloroplasts exhibited chlorophyll autofluorescence and formed a monophyletic psbA gene clade that suggested Esoptrodinium possesses inherited, peridinoid‐type plastids. One isolate with cryptic, barely visible plastids lacked detectable chlorophyll and exhibited an apparent loss‐of‐function mutation in psbA, indicating the presence of nonphotosynthetic plastids. The other isolate that lacked visible chloroplasts lacked both detectable chlorophyll and an amplifiable psbA sequence. The results demonstrate mixotrophy quantitatively for the first time in a freshwater dinoflagellate, as well as apparent within‐clade loss of phototrophy along with a correlated mutation sufficient to explain that phenotype. Phototrophy is a variable trait in Esoptrodinium; further study is required to determine if this represents an inter‐ or intraspecific (allelic) characteristic in this taxon.     

Iningainema pulvinus gen nov., sp nov. (Cyanobacteria,Scytonemataceae) a new nodularin producer from Edgbaston Reserve,north-eastern Australia

A new nodularin producing benthic cyanobacterium Iningainema pulvinus gen nov., sp nov. was isolated from a freshwater ambient spring wetland in tropical, north-eastern Australia and characterised using combined morphological and phylogenetic attributes. It formed conspicuous irregularly spherical to discoid, blue-green to olive-green cyanobacterial colonies across the substratum of shallow pools. Morphologically Iningainema is most similar to Scytonematopsis Kiseleva and Scytonema Agardh ex Bornet & Flahault. All three genera have isopolar filaments enveloped by a firm, often layered and coloured sheath; false branching is typically geminate, less commonly singly. Phylogenetic analyses using partial 16S rRNA sequences of three clones of Iningainema pulvinus strain ES0614 showed that it formed a well-supported monophyletic clade. All three clones were 99.7–99.9% similar, however they shared less than 93.9% nucleotide similarity with other cyanobacterial sequences including putatively related taxa within the Scytonemataceae. Amplification of a fragment of the ndaF gene involved in nodularin biosynthesis from Iningainema pulvinus confirmed that it has this genetic determinant. Consistent with these results, analysis of two extracts from strain ES0614 by HPLC–MS/MS confirmed the presence of nodularin at concentrations of 796 and 1096 μg g⁻¹ dry weight. This is the third genus of cyanobacteria shown to produce the cyanotoxin nodularin and the first report of nodularin synthesis from the cyanobacterial family Scytonemataceae. These new findings may have implications for the aquatic biota at Edgbaston Reserve, a spring complex which has been identified as a priority conservation area in the central Australian arid and semiarid zones, based on patterns of endemicity.     

First record of the bacterial endosymbiont Wolbachia for phytophagous hoverflies from genus Merodon (Diptera: Syrphidae)

Wolbachia is a widespread bacterial endosymbiont among arthropod species. It influences the reproduction of the host species and also mitochondrial DNA diversity. Until now there were only a few studies that detected Wolbachia infections in hoverflies (Diptera: Syrphidae), and this is the first broader study with the aim of examining the incidence of Wolbachia in the hoverfly genus Merodon. The obtained results indicate an infection rate of 96% and the presence of both Wolbachia supergroup A and B, which are characteristic for most of the infected arthropod species. Additionally, the presence of multiple Wolbachia strains in the Merodon aureus group species was detected and the mitochondrial DNA COI‐based relationships of the group are discussed in the light of infection. Finally, we discuss plant‐mediated horizontal transmission of Wolbachia strains among the studied hoverfly species.     

Long‐term balanced fertilization increases the soil microbial functional diversity in a phosphorus‐limited paddy soil

The influence of long‐term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22‐year period. These included a control without fertilizers; chemical nitrogen fertilizer (N); N and phosphate (NP); N and potassium (NK); and N, P and K (NPK). Based on 16S rRNA gene data, both species evenness and key genera were affected by P fertilization. Functional gene array‐based analysis revealed that long‐term fertilization significantly changed the overall microbial functional structures. Chemical fertilization significantly increased the diversity and abundance of most genes involved in C, N, P and S cycling, especially for the treatments NK and NPK. Significant correlations were found among functional gene structure and abundance, related soil enzymatic activities and rice yield, suggesting that a fertilizer‐induced shift in the microbial community may accelerate the nutrient turnover in soil, which in turn influenced rice growth. The effect of N fertilization on soil microbial functional genes was mitigated by the addition of P fertilizer in this P‐limited paddy soil, suggesting that balanced chemical fertilization is beneficial to the soil microbial community and its functions.