Phylogenetic relationships within the class Spirotrichea (Ciliophora) inferred from small subunit rRNA gene sequences

The small subunit rDNAs of five species belonging to the Euplotidae and eight species of the Oxytrichidae were sequenced to obtain a more detailed picture of the phylogenetic relationships within the Spirotrichea (Ciliophora). Various tree reconstruction algorhythms yielded nearly identical topologies. All Euplotidae were separated from the other Spirotrichea by a deep split. Further, a large genetic distance between the marine genus Moneuplotes and the freshwater species of Euplotoides was found. Differences between the methods used occurred only within the Oxytrichidae. Whereas the monophyly of the Stylonychinae was supported in all trees, the monophyly of the Oxytrichinae was not. However, the molecular data support the morphological and ontogenetic evidence that the pattern of 18 frontal-ventral-transversal cirri evolved in the stemline of the Oxytrichidae and was modified several times independently. Our results are also in agreement with taxonomic revisions: the separation of both Sterkiella nova from Oxytricha and Tetmemena pustulata from Stylonychia.     

Phylogenetic analysis of ten black yeast species using nuclear small subunit rRNA gene sequences

The nuclear small subunit rRNA genes of authentic strains of the black yeastsExophiala dermatitidis, Wangiella dermatitidis, Sarcinomyces phaeomuriformis, Capronia mansonii, Nadsoniella nigra var.hesuelica, Phaeoannellomyces elegans, Phaeococcomyces exophialae, Exophiala jeanselmei var.jeanselmei andE. castellanii were amplified by PCR and directly sequenced. A putative secondary structure of the nuclear small subunit rRNA ofExophiala dermatitidis was predicted from the sequence data. Alignment with corresponding sequences fromNeurospora crassa andAureobasidium pullulans was performed and a phylogenetic tree was constructed using the neighbor-joining method. The obtained topology of the tree was confirmed by bootstrap analysis. Based upon this analysis all fungi studied formed a well-supported monophyletic group clustering as a sister group to one group of the Plectomycetes (Trichocomaceae and Onygenales). The analysis confirmed the close relationship postulated betweenExophiala dermatitidis, Wangiella dermatitidis andSarcinomyces phaeomuriformis. This monophyletic clade also contains the teleomorph speciesCapronia mansonii thus confirming the concept of a teleomorph connection of the genusExophiala to a member of the Herpotrichiellaceae. However,Exophiala castellanii did not belong to this clade. Therefore, this species is not the anamorph ofCapronia mansonii as it was postulated.     

Molecular phylogeny of the Heterotrichea (Ciliophora, Postciliodesmatophora) based on small subunit rRNA gene sequences

A comprehensive molecular analysis of the phylogenetic relationships within the Heterotrichea including all described families is still lacking. For this reason, the complete nuclear small subunit (SSU) rDNA was sequenced from further representatives of the Blepharismidae and the Stentoridae. In addition, the SSU rDNA of a new, undescribed species of the genus Condylostomides (Condylostomatidae) was sequenced. The detailed phylogenetic analyses revealed a consistent branching pattern: while the terminal branches are generally well resolved, the basal relationships remain unsolved. Moreover, the data allow some conclusions about the macronuclear evolution within the genera Blepharisma, Stentor, and Spirostomum suggesting that a single, compact macronucleus represents the ancestral state.     

Phylogeny of six oligohymenophoreans (Protozoa, Ciliophora) inferred from small subunit rRNA gene sequences

The small subunit rRNA (SSrRNA) genes of six marine oligohymenophoreans, namely Uronemella filificum , Schizocalyptra sp.-WYG07060701, Schizocalyptra aeschtae , Pleuronema sinica , P. czapikae and Paratetrahymena sp., were sequenced. Phylogenetic trees were constructed with four different methods to assess the inter- and intrageneric relationships among the scuticociliates and the phylogenetic assignment of the order Loxocephalida. The SSrRNA phylogeny indicates that: (i) Paratetrahymena is most closely related to Cardiostomatella ; (ii) the order Loxocephalida and the family Uronematidae both appear to be polyphyletic; (iii) the order Philasterida is a well-defined taxon; (iv) Cyclidium porcatum falls outside the order Pleuronematida in all analyses; (v) the validity of the genus Uronemella is confirmed; (vi) Schizocalyptra is a member of the family Pleuronematidae. Furthermore, the predicted secondary structures of the variable region 4 of the SSrRNA gene sequences show that the size of the terminal bulge in Helix E23–7 is probably different for the orders Philasterida and Pleuronematida. Also, compared to Uronema and Homalogastra , Uronemella has distinct patterns in Helices E23–1, E23–7, E23–8 and E23–9.     

Phylogenetic relationships of the subclass Peritrichia (Oligohymenophorea, Ciliophora) inferred from small subunit rRNA gene sequences

The phylogenetic relationships among peritrichs remain unresolved. In this study, the complete small subunit rRNA (SSrRNA) gene sequences of seven species (Epistylis galea, Campanella umbellaria, Carchesium polypinum, Zoothamnium arbuscula, Vaginicola crystallina, Ophrydium versatile, and Opercularia microdiscum) were determined. Trees were constructed using distance-matrix, maximum-likelihood and maximum-parsimony methods, all of which strongly supported the monophyly of the subclass Peritrichia. Within the peritrichs, 1) E. galea grouped with Opercularia microdiscum and Campanella umbellaria but not the other Epistylis species, which indicates that the genus Epistylis might not be monophyletic; 2) the topological position of Carchesium and Campanella suggested that Carchesium should be placed in the family Zoothamniidae, or be elevated to a higher taxonomic rank, and that Campanella should be independent of the family Epistylididae, and probably be given a new rank; and 3) Opisthonecta grouped strongly with Astylozoon, which suggested that Opisthonecta species were not the ancestors of the stalked peritrichs.     

Phylogenetic relationships of the Subclass Peniculia (Oligohymenophorea, Ciliophora) inferred from small subunit rRNA gene sequences

Peniculine ciliates have been recognized as a distinct higher taxon of ciliates for almost 50 years. However, phylogenetic relationships within the Subclass Peniculia are still unsettled. To contribute to our understanding of their phylogeny and provide evidence for the position of Urocentrum turbo, we sequenced its small subunit (SS) rRNA gene and the SSrRNA genes from Lembadion bullinum, Frontonia sp., Paramecium caudatum, Paramecium multimicronucleatum, Paramecium putrinum, and Paramecium woodruffi. Urocentrum turbo was the only one of these species not to exhibit a shortened Helix E10_1, which we conclude characterizes the "higher" peniculines. Except for U. turbo, the peniculines are strongly supported as a monophyletic clade with Lembadion, Frontonia, and Paramecium species forming separate and strongly supported clades by bootstrap analysis using distance matrix, maximum parsimony, and maximum likelihood methods. Urocentrum turbo is associated with different lineages, depending upon the analysis used. The Paramecium species form at least four clades with the Paramecium aurelia subgroup being the most derived. We conclude that the Subclass Peniculia should be divided into two orders, the Order Urocentrida and Order Peniculida, with the latter order having two suborders, the Suborder Frontoniina and Peniculina. We place U. turbo with the peniculines because of shared morphological and stomatogenetic features.     

Species of tetrahymena identical by small subunit rRNA gene sequences are discriminated by mitochondrial cytochrome c oxidase I gene sequences

The mitochondrial cytochrome c oxidase 1 (CO1) genes of two isolates of each of the seven mating types of Tetrahymena thermophila were sequenced and found to differ by < 1% in nucleotide sequence and to be identical by putative protein sequence. As this gene was highly conserved in this species, the CO1 gene sequence was determined for four pairs of Tetrahymena species identical in their small subunit rRNA gene sequences. The following pairs of species showed from 1% to 12% divergence at the nucleotide level, enabling discrimination of all these species: (1) Tetrahymena pyriformis strain T and Tetrahymena setosa strain HZ-1; (2) Tetrahymena canadensis strain UM1215 and Tetrahymena rostrata strain ID-3; (3) Tetrahymena pigmentosa strain UM1285 and Tetrahymena hyperangularis strain EN112; and (4) Tetrahymena tropicalis strain TC-105 and Tetrahymena mobilis. However, because of the synonymous nature of the majority of substitutions, the pairs of species were identical based on the putative protein sequence.     

Phylogenetic relationships of the genus Paramecium inferred from small subunit rRNA gene sequences

The genus Paramecium includes species that are well known and very common in freshwater environments. Species of Paramecium are morphologically divided into two distinct groups: the "bursaria" subgroup (foot-shaped) and the "aurelia" subgroup (cigar-shaped). Their placement within the class Oligohymenophorea has been supported by the analysis of the small subunit rRNA gene sequence of P. tetraurelia. To confirm the stability of this placement and to resolve relationships within the genus, small subunit rRNA gene sequences of P. bursaria, P. calkinsi, P. duboscqui, P. jenningsi, P. nephridiatum, P. primaurelia, and P. polycaryum were determined and aligned. Trees constructed using distance-matrix, maximum-likelihood, and maximum-parsimony methods all depicted the genus as a monophyletic group, clustering with the other oligohymenophorean taxa. Within the Paramecium clade, P. bursaria branches basal to the other species, although the remaining species of the morphologically defined "bursaria" subgroup do not group with P. bursaria, nor do they form a monophyletic subgroup. However, the species of the "aurelia" subgroup are closely related and strongly supported as a monophyletic group.     

Molecular phylogenetic study of the heterotrophic dinoflagellate genus Protoperidinium (Dinophyceae) inferred from small subunit rRNA gene sequences

In the present study, we investigated the intrageneric and intergeneric phylogenetic relationships of the heterotrophic marine dinoflagellate genus Protoperidinium. Using single‐cell polymerase chain reaction methods, we determined small subunit ribosomal RNA gene sequences for 10 Protoperidinium species belonging to four sections and two subgenera. Phylogenetic trees were constructed using maximum parsimony, neighbor joining and maximum likelihood methods. We found intraspecific variability of small subunit rDNA sequences in Protoperidinium conicum (Gran) Balech, Protoperidinium crassipes (Kofoid) Balech and Protoperidinium denticulatum (Gran et Braarud) Balech, but not in other species. The small subunit rDNA phylogeny revealed that the genus is monophyletic, but its phylogenetic position within the Dinophyceae could not be determined because of ambiguous basal topologies. Within the genus Protoperidinium, species of the subgenus Archaeperidinium with two anterior intercalary plates (2a) were shown to be monophyletic, but species of the subgenus Protoperidinium with three anterior intercalary plates (3a) were resolved as paraphyletic. The sections Avellana, Divergentia and Protoperidinium were shown to be monophyletic, while the section Conica was paraphyletic. Based on the trees obtained in the present study, most of the traditionally defined sections are supported by molecular phylogeny. It was also indicated that the section Avellana evolved from one of the Conica‐type dinoflagellates.     

The current status of the small subunit rRNA phylogeny of the coccidia (Sporozoa)

There is no current comprehensive assessment of the molecular phylogeny of the coccidia, as all recently published papers either deal with subsets of the taxa or sequence data, or provide non-robust analyses. Here, we present a comprehensive and consistent phylogenetic analysis of the available data for the small-subunit ribosomal RNA gene sequence, including a number of taxa not previously studied, based on a Bayesian tree-building analysis and the covariotide model of evolution. The assumptions of the analysis have been rigorously tested, and the benefits and limitations highlighted. Our results provide support for a number of prior conclusions, including the monophyly of the families Sarcocystidae (cyst-forming coccidia) and Eimeriidae (oocyst-forming coccidia), but with bird-host Isospora species in the Eimeriidae and mammal-host species in the Sarcocystidae. However, it is clear that a number of previously reported relationships are dependent on the evolutionary model chosen, such as the placements of Goussia janae, Lankesterella minimia and Caryospora bigenetica. Our results also confirm the monophyly of the subfamilies Toxoplasmatinae and Sarcocystinae, but only some of the previously reported groups within these subfamilies are supported by our analysis. Similarly, only some of the previously reported groups within the Eimeriidae are supported by our analysis, and the genus Eimeria is clearly paraphyletic. There are unambiguous patterns of host-parasite relationship within the coccidia, as most of the well-supported groups have a consistent and restricted range of hosts, with the exception of the Toxoplasmatinae. Furthermore, the previously reported groups for which we found no support all have a diverse range of unrelated hosts, confirming that these are unlikely to be natural groups. The most interesting unaddressed questions may relate to Isospora, which has the fewest available sequences and host-parasite relationships apparently not as straightforward as elsewhere within the suborder.     

Molecular phylogenetic position of the genera Stephanonympha and Caduceia (Parabasalia) inferred from nuclear small subunit rRNA gene sequences

Nuclear small subunit (SSU) rRNA gene sequences were obtained by polymerase chain reaction from trichomonad symbionts of termites that belong to the Devescovinidae (Caduceia versatilis) and polymastigont Calonymphidae (Stephanonympha nelumbium). The unidentified SSU rRNA sequence Nk3, previously obtained from the termite Neotermes koshunensis, has also been shown to derive from a Stephanonympha sp. by in situ hybridization. These sequences were analysed in a broad phylogeny including nearly all identified parabasalid sequences available in the databases, and some as yet unidentified sequences likely deriving from the new order Cristamonadida (Devescovinidae, Calonymphidae, and hypermastigids Lophomonadida). A global phylogeny of parabasalids reveals a partial agreement between the clades identified in this work and the last classification of this phylum into four orders. However, this classification is still incongruent with our data and new taxonomic considerations are proposed. The analysis confirms the monophyly of the Cristamonadida and separates this order into two groups: the first unites nearly all the Devescovinidae including Caduceia and the Calonymphidae Coronympha and Metacoronympha, whereas the second group is composed of a few Devescovinidae, Lophomonadida, and Calonymphidae such as Stephanonympha. Caduceia is closely related to Devescovina, corroborating the marked morphological similarity between these two genera whereas Stephanonympha groups together with the Calonymphidae Snyderella and Calonympha. These data also confirm the polyphyly of the families Devescovinidae and Calonymphidae and support the arrangement of the axostyle-pelta complexes as a valuable character for taxonomic considerations within the Calonymphidae.     

Effects of arbuscular mycorrhiza (AM) on health ofLinum usitatissimum L. infected by fungal pathogens

Effects of arbuscular mycorrhizal (AM) symbiosis on health ofLinum usitatissimum infected by fungal pathogens were investigated exemplarily. Physiological and biochemical analyses were done to explain the mechanisms underlying the AM effects. AM plants showed increased resistance against the wilt pathogen (Fusarium oxysporum f. sp.lini), the level of this effects depended on the plant cultivars which all showed the same level of root colonization by arbuscular mycorrhizal fungi (AMF). In contrary to that, AM plants were highly susceptible against the shoot pathogenOidium lini, but they suffered less than non-AM plants in terms of shoot fresh weight, CO₂ assimilation and content of sucrose in shoot apex. This indicates that AM not only activates resistance mechanisms but also can induce tolerance against pathogens. The concentration of phytohormones such as auxin- and gibberellin-like substances were increased in shoots of AM plants. In roots the ethylene production was increased, too. Furthermore the content and composition of free sterols were highly altered in leaves of AM plants. Root infection by AMF caused an increased respiratory activity and a reduced degree of DNA methylation, but both modifications only occurred in infected root parts indicating an increasing gene activity. The presented results suggest that nearly all parts of a plant are influenced by AM but not in the same manner. In the case of mildewed linseed the effect of AM on plant health was impressing, it indicates that AM has an ability to induce tolerance.     

A phylogenetic reconsideration of suctorian ciliates (Protista,Ciliophora, Phyllopharyngea) based on small subunit rRNA gene sequences

Compared with other ciliated protozoa, molecular studies of phylogenetic relationships within the subclass Suctoria are rare. In this work, phylogenetic analyses focusing on this group were performed based on all data available. In addition, the small subunit ribosomal RNA (SSU rRNA) genes of three suctorian ciliates (Acineta compressa, Acineta tuberosa and Paracineta limbata) were newly sequenced. Furthermore, the putative secondary structures of the variable region 2 of the SSU rRNA gene were predicted and compared within the Suctoria. Our results show that (i) there is support for the monophyly of the subclass Suctoria, which is a sister clade to the cyrtophorids; (ii) based on combined morphologic and molecular features, we propose the following evolutionary routine within the Suctoria: Exogenina – Evaginogenina – Endogenina; (iii) the similarities of the secondary structures of the V2 region and the SSU rRNA gene sequences within the subclass Suctoria are consistent with the branching of the phylogenetic lineages.     

The phylogeny of colpodellids (Alveolata) using small subunit rRNA gene sequences suggests they are the free-living sister group to apicomplexans

In an attempt to reconstruct early alveolate evolution, we have examined the phylogenetic position of colpodellids by analyzing small subunit rDNA sequences from Colpodella pontica Myl'nikov 2000 and Colpodella sp. (American Type Culture Collection 50594). All phylogenetic analyses grouped the colpodellid sequences together with strong support and placed them strongly within the Alveolata. Most analyses showed colpodellids as the sister group to an apicomplexan clade, albeit with weak support. Sequences from two perkinsids, Perkinsus and Parvilucifera, clustered together and consistently branched as the sister group to dinoflagellates as shown previously. These data demonstrate that colpodellids and perkinsids are plesiomorphically similar in morphology and help provide a phylogenetic framework for inferring the combination of character states present in the last common ancestor of dinoflagellates and apicomplexans. We can infer that this ancestor was probably a myzocytotic predator with two heterodynamic flagella, micropores, trichocysts, rhoptries, micronemes, a polar ring, and a coiled open-sided conoid. This ancestor also very likely contained a plastid, but it is presently not certain whether it was photosynthetic, and it is not clear whether extant perkinsids or colpodellids have retained the organelle.     

higher-order phylogeny of plasmodial slime molds (Myxogastria) based on elongation factor 1-A and small subunit rRNA gene sequences

The Myxogastria are common soil microorganisms with a life cycle comprised of a plasmodial trophic stage and large fruiting bodies generally visible with the unaided eye. Until now, their classification has been based exclusively on a combination of morphological, ultrastructural, and developmental characters. Our study is the first attempt to examine phylogenetic relationships among these taxa using molecular data. Partial small-subunit ribosomal RNA and/or elongation factor 1-alpha gene sequences were obtained from eleven, mostly field-collected species representing the five orders of Myxogastria. Nineteen sequences were obtained and subjected to phylogenetic analysis together with 10 sequences available from GenBank. Separate and combined analyses of the two data sets support the division of Myxogastria into three distinct groups. The most basal clade consists of the Echinosteliales, an order considered to have affinities with Protostelia. The three species examined possess unpigmented or slightly pigmented spores. The second group consists of Liceales and Trichiales, taxa characterized by the presence of clear, but pigmented, spores. The third group consists of the two remaining orders, Physarales and Stemonitales, both possessing dark spores. This suggests that spore pigmentation is an evolutionarily conservative character in myxogastrians, and that the simple morphology of echinostelids is not a derived feature.     

Phylogenetic analysis of 16S rRNA gene sequences reveals distal gut bacterial diversity in wild wolves (Canis lupus)

The aim of this study was to describe the microbial communities in the distal gut of wild wolves (Canis lupus). Fecal samples were collected from three healthy unrelated adult wolves captured at the nearby of Dalai Lake Nature Reserve in Inner Mongolia of China. The diversity of fecal bacteria was investigated by constructing PCR-amplified 16S rRNA gene clone libraries using the universal bacterial primers 27 F and 1493 R. A total of 307 non-chimeric near-full-length 16S rRNA gene sequences were analyzed and 65 non-redundant bacteria phylotypes (operational taxonomical units, OTUs) were identified. Seventeen OTUs (26%) showed less than 98% sequence similarity to 16S rRNA gene sequences were reported previously. Five different bacterial phyla were identified, with the majority of OTUs being classified within the phylum Firmicutes (60%), followed by Bacteroidetes (16.9%), Proteobacteria (9.2%), Fusobacteria (9.2%) and Actinobacteria (4.6%). The majority of clones fell within the order Clostridiales (53.8% of OTUs). It was predominantly affiliated with five families: Lachnospiraceae was the most diverse bacterial family in this order, followed by Ruminococcaceae, Clostridiaceae, Peptococcaceae and Peptostreptococcaceae.     

Partial small subunit (18S) rRNA gene sequences from fish parasites of the families Lepocreadiidae and Fellodistomidae (Digenea) and their use in phylogenetic analyses

Digeneans of the families Lepocreadiidae and Fellodistomidae are common parasites of shallow and deep-water marine fishes. Worms recovered from these contrasting environments may be indistinguishable or very similar morphologically and little is known concerning their inter-relationships. To investigate the systematic status of these forms, partial sequences from a small subunit 18S rRNA gene were generated from four species of lepocreadiids (Lepidapedon elongatum, L. gaevskayae, L. rachion and Opechona bacillaris) and two fellodistomids (Fellodistomum fellis and Steringophorus agnotus). Approximately 1,637 bases were sequenced for L. elongatum, L. rachion and F. fellis. A comparison of these sequences identified regions which varied between the two families. As a result, two regions were identified as containing potential phylogenetically informative sites and sequenced from the remaining species. Analyses of these regions by both maximum parsimony and distance methods showed that nucleic acid sequence data can be used to resolve the two families. The results indicate that 18S rRNA sequences are likely to be more satisfactory at resolving higher levels of phylogeny, i.e. at the family level, than at the generic level due to the similarity shown between the sequences of congeners.     

Phylogeny of the Stichotrichia (Ciliophora; Spirotrichea) reconstructed with nuclear small subunit rRNA gene sequences: discrepancies and accordances with morphological data

The Stichotrichia, known as an especially various and taxonomically difficult group, were intensely studied with morphological, morphogenetic, and molecular methods in the last years. Nevertheless, a consistent classification is lacking and several important questions about the phylogenetic relationships within this group remain unsolved. In order to gain deeper insights into these relationships, the nuclear small subunit rRNA genes of seven species of the Stichotrichia, representatives of the families Oxytrichidae, Amphisiellidae, and Pseudourostylidae, were phylogenetically analysed. Although our analyses resulted in a poor resolution of the phylogenetic relationships, some conclusions can be drawn. Firstly, following the current classification systems the Oxytrichidae as well as their subfamilies seem to be paraphyletic and the basic 18 FVT cirral pattern has been modified several times independently. Secondly, sequence analyses of several Oxytricha species resulted in a high molecular diversity, which does not support monophyly of this genus. Thirdly, several families of the order Urostylida (Urostylidae, Pseudokeronopsidae, and Pseudourostylidae) also do not form monophyletic groups.     

Phylogenetic relationships of the subclass peritrichia (Oligohymenophorea, Ciliophora) with emphasis on the genus Epistylis, inferred from small subunit rRNA gene sequences

The peritrichs have been recognized as a higher taxon of ciliates since 1968. However, the phylogenetic relationships among them are still unsettled, and their placement within the class Oligohymenophorea has only been supported by the analysis of the small subunit rRNA gene sequence of Opisthonecta henneguyi. DNA was isolated directly from field-sampled species for PCR, and was used to resolve relationships within the genus Epistylis and to confirm the stability of the placement of peritrichs. Small subunit rRNA gene sequences of Epistylis plicatilis, Epistylis urceolata, Epistylis chrysemydis, Epistylis hentscheli, Epistylis wenrichi, and Vorticella campanula were sequenced and analyzed using both distance-matrix and maximum-parsimony methods. In phylogenetic trees, the monophyly of both the genus Episrylis and the subclass Peritrichia was strongly supported, while V. campanula clustered with Vorticella microstoma. The topology in which E. plicatilis and E. hentscheli formed a strongly supported sister clade to E. urceolata, E. chrysemydis, and E. wenrichi was consistent with variations in the thickness of the peristomial lip. We concluded that the peristomial area, especially the peristomial lip, might be the important phylogenetic character within the genus Epistylis.     

Bacterial diversity in saline-alkali ponds rearing common carp (Cyprinus carpio) as revealed by 16S rRNA gene sequences

The bacterial diversity in saline-alkali ponds rearing common carp was investigated using the 16S rRNA gene clone library technique. Phylogenetic analysis of the most common and dominant sequences recovered indicated that these sequences fell into the following major lineages, including Proteobacteria (α-, β-, γ-), Actinobacteria, Cyanobacteria, Planctomycetes, Fibrobacteres, Bacteroidetes, Chloroflexi, and unclassified bacteria. Sequence analysis showed that the bacterial diversity was abundant, and the sequences belonging to β-Proteobacteria, α-Proteobacteria and Actinobacteria were predominant. The most sequences in the saline-alkali rearing ponds exhibited low similarity with known bacterial 16S rRNA genes, suggesting that these sequences may represent novel bacteria. In addition, the majority of our sequences were most closely affiliated with sequences retrieved from inland waters of China. These results suggest that the saline-alkali ponds rearing common carp are specific ecologic niches and the distribution of the bacteria may be influenced by geographical factors. This study reports the bacterial diversity in saline-alkali ponds rearing common carp by the culture-independent technique for the first time; therefore, it provides important information for understanding the microbial ecology in saline-alkali rearing ponds and managing the microbial community composition to promote and maintain the health of aquaculture environments.