Meiobenthos of hypersaline tropical mangrove sediment in relation to spring tide inundation

Tropical intertidal sediments often contain porewater of relatively high salinity, especially in areas exposed to longer periods without seawater inundation and high evaporation. Such an area exists on the west coast of Zanzibar: a high intertidal mangrove plateau, flooded only during spring high tides, with sediment porewater salinities commonly exceeding 100 ppt. A field survey was conducted in this area to examine variations in population density of major meiofaunal taxa and the assemblage structure of free-living marine nematodes during spring-neap tidal cycles. Samples were taken on seven occasions for two months, starting from the end of the rainy season. Porewater salinity remained high throughout the sampling period, ranging from 89 to 160 ppt. Neither spring tide inundation nor heavy rains lowered the salinity markedly. The meiofauna consisted only of four taxa, present on all sampling occasions: nematodes, harpacticoid copepods, plathyhelminthes and chironomids. Densities in surface sediments (0–5 cm) were low compared to other mangrove areas, ranging from 271 to 656 animals 10 cm^-2 with nematodes dominant on all sampling occasions (58–87%). Density fluctuations could not be explained by the effects of spring tide inundation, but the meiofauna showed significant correlations with grain size and organic material. Despite the wide range of salinity, only the numbers of chironomids were negatively correlated with increased salinity. Nematode species diversity was low in all samples, although altogether 28 species were recorded in the samples. Four species occurred in more than 50% of the samples (Microlaimus sp. (100%), Metalinhomoeus sp. (76%), Daptonema sp.l (56%), Chromadorina sp. (56%)) while 12 species were found only in one or two samples. Multidimensional scaling ordination (MDS) of the nematode species abundance data indicated little effects of spring tide inundation on the assemblage structure, but rather a successive change from wet to dry season with a reduction in species diversity and increased numbers of the dominant nematode species Microlaimus sp.     

Adaptations by macroalgae to low carbon availability. I. A buffer system in Ascophyllum nodosum, associated with photosynthesis

Abstract The exchange of CO₂, H⁺ and O₂ between seawater and the intertidal brown macroalga Ascophyllum nodosum (L.) Le Jolis were measured in a flowthrough system. While the algae were kept in darkness, seawater with artificially increased alkalinity and pH at 9.85, was alternated with ‘normal’ seawater at pH 8.0. A proton buffering system, with capacity to release and reabsorb about 20 μmol protons per gram alga (fresh weight) was revealed. As the algae were returned to the ‘normal’ seawater, the kinetics of proton reabsorbtion indicated that a proton uptake was gradually induced. This proton uptake, which was not connected to ion exchange in the cell wall, reached its maximum after 12 h. If subjected to high alkalinity seawater in the light, A. Nodosum for a certain period of time was capable of carrying out O, evolution in excess of the import of inorganic carbon. This ‘photosynthetic buffering capacity’ amounted to about 17 μmol O; per gram alga. Besides depending on a buffer of photorcducible substances, this ‘photosynthetic buffering capacity’ appeared to be functionally connected with the proton buffer. The time course for the discharge of the ‘photosynthetic buffer system’ and for the reabsorbtion of protons into the proton buffer (about 6h for 90× of the capacity at a temperature of 6°C) suggests that the ‘photosynthetic buffer system’ has a functional importance in the adaptation of A. nodosum to intertidal regions. The function of the buffer system is discussed in relation to the crassulacean acid metabolism (CAM)-like characteristics recently shown for the intertidal brown algal family Fucaceae.     

Molecular diversity of arbuscular mycorrhizal fungi in onion roots from organic and conventional farming systems in the Netherlands

Diversity and colonization levels of naturally occurring arbuscular mycorrhizal fungi (AMF) in onion roots were studied to compare organic and conventional farming systems in the Netherlands. In 2004, 20 onion fields were sampled in a balanced survey between farming systems and between two regions, namely, Zeeland and Flevoland. In 2005, nine conventional and ten organic fields were additionally surveyed in Flevoland. AMF phylotypes were identified by rDNA sequencing. All plants were colonized, with 60% for arbuscular colonization and 84% for hyphal colonization as grand means. In Zeeland, onion roots from organic fields had higher fractional colonization levels than those from conventional fields. Onion yields in conventional farming were positively correlated with colonization level. Overall, 14 AMF phylotypes were identified. The number of phylotypes per field ranged from one to six. Two phylotypes associated with the Glomus mosseae–coronatum and the G. caledonium–geosporum species complexes were the most abundant, whereas other phylotypes were infrequently found. Organic and conventional farming systems had similar number of phylotypes per field and Shannon diversity indices. A few organic and conventional fields had larger number of phylotypes, including phylotypes associated with the genera Glomus-B, Archaeospora, and Paraglomus. This suggests that farming systems as such did not influence AMF diversity, but rather specific environmental conditions or agricultural practices. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Authors Guillermo A. Galván and István Parádi contributed equally to this research and share first co-authorship.     

Distribution and phylogenetic diversity of cbbM genes encoding RubisCO form II in a deep-sea hydrothermal field revealed by newly designed PCR primers

To investigate the phylogenetic diversity of putative chemolithoautotrophs possessing the RubisCO form II gene (cbbM) in various environments, we designed a new PCR primer set targeting this gene. The primer set was designed to cover more diverse and longer sequences of cbbM genes than those reported previously. We analyzed various samples (i.e., benthic sands, basement rocks, sulfide chimneys, vent fluids and overlying bottom seawater) collected in a deep-sea hydrothermal field of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific, by PCR-based analysis using the designed primer set. Most of the cbbM phylotypes recovered from the liquid samples were related to those of the SUP05 group that belongs to the Gammaproteobacteria and includes putative sulfide-oxidizing chemolithoautotrophs. In contrast, the cbbM phylotypes recovered from the solid samples were related to environmental clones with low similarity (74–90%) and not closely related to the SUP05 group (69–74%). The cbbM phylotypes recovered from the liquid samples were different from those of the solid samples. Furthermore, the cbbM phylotypes recovered from the solid samples were different from each other. Our results expand knowledge of the phylogenetic diversity and distribution of putative chemolithoautotrophs possessing RubisCO form II cbbM genes in deep-sea hydrothermal fields.     

Probing the archaeal diversity of a mixed thermophilic bioleaching culture by TGGE and FISH

The archaeal community present in a sample of Mixed Thermophilic Culture-B (MTC-B) from a laboratory-scale thermophilic bioleaching reactor was investigated by temperature gradient gel electrophoresis (TGGE) and fluorescence in situ hybridisation (FISH). Both techniques were specifically adapted for use on native state bioleaching samples, with a view to establishing convenient means for monitoring culture composition. Using the TGGE protocol developed, the relative species composition of the thermophilic bioleaching sample was analysed, and included four phylotypes belonging to the Sulfolobales, which were related to Stygiolobus azoricus, Metallosphaera sp. J1, Acidianus infernus and Sulfurisphaera ohwakuensis. However, the St. azoricus-like phylotype was difficult to resolve and some micro-heterogeneity was observed within this phylotype. Specific FISH probes were designed to qualitatively assess the presence of the phylotypes in MTC-B. The sample was dominated by Sf. ohwakuensis-like Archaea. In addition, the St. azoricus-like, Metallosphaera species-like and Acidianus species-like cells appeared in similar low abundance in the community. Most strikingly, FISH identified Sulfolobus shibatae-like cells present in low numbers in the sample even though these were not detected by PCR-dependent TGGE. These results highlight the importance of using more than one molecular technique when investigating the archaeal diversity of complex bioleaching reactor samples.     

Leucine‐to‐carbon empirical conversion factor experiments: does bacterial community structure have an influence?

The suitability of applying empirical conversion factors (eCFs) to determine bacterial biomass production remains unclear because seawater cultures are usually overtaken by phylotypes that are not abundant in situ. While eCFs vary across environments, it has not been tested whether differences in eCFs are driven by changes in bacterial community composition or by in situ environmental conditions. We carried out seawater cultures throughout a year to analyse the correlation between eCFs and bacterial community structure, analysed by catalysed reporter deposition fluorescence in situ hybridization. Gammaproteobacteria usually dominated seawater cultures, but their abundance exhibited a wide range (25–73% of cell counts) and significantly increased with inorganic nutrient enrichment. Flavobacteria were less abundant but increased up to 40% of cells counts in winter seawater cultures, when in situ chlorophyll a was high. The correlations between eCFs and the abundance of the main broad phylogenetic groups (Gamma‐, Alphaproteobacteria and Flavobacteria) were significant, albeit weak, while more specific groups (Alteromonadaceae and Rhodobacteraceae) were not significantly correlated. Our results show that the frequent development of the fast‐growing group Alteromonadaceae in seawater cultures does not strongly drive the observed variations in eCFs. Rather, the results imply that environmental conditions and the growth of specific phylotypes interact to determine eCFs.     

Rapid shifts in picoeukaryote community structure in response to ocean acidification

Rapid shifts in picoeukaryote community structure were observed during a CO₂ perturbation experiment in which we followed the development of phytoplankton blooms in nutrient-amended mesocosms under the present day or predicted future atmospheric pCO₂ (750 μatm, seawater pH 7.8). Analysis of rbcL clone libraries (encoding the large subunit of RubisCO) and specific quantitative PCR assays showed that two prasinophytes closely related to Micromonas pusilla and Bathycoccus prasinos were present, but responded very differently to high CO₂/acidification. We found that the abundance of Micromonas-like phylotypes was significantly higher (>20-fold) under elevated CO₂/low pH, whereas the Bathycoccus-like phylotypes were more evenly distributed between treatments and dominated the prasinophyte community under ambient conditions.     

Diversity of the major capsid genes (g23) of T4-like bacteriophages in the eutrophic Lake Kotokel in East Siberia, Russia

Numerous studies revealed high diversity of T4-like bacteriophages in various environments, but so far, little is known about T4-like virus diversity in freshwater bodies, particularly in eutrophic lakes. The present study was aimed at elucidating molecular diversity of T4-like bacteriophages in eutrophic Lake Kotokel located near Lake Baikal by partial sequencing of the major capsid genes (g23) of T4-like bacteriophages. The majority of g23 fragments from Lake Kotokel were most similar to those from freshwater lakes and paddy fields. Despite the proximity and direct water connection between Lake Kotokel and Lake Baikal, g23 sequence assemblages from two lakes were different. UniFrac analysis showed that uncultured T4-like viruses from Lake Kotokel tended to cluster with those from the distant lake of the same trophic status. This fact suggested that the trophic conditions affected the formation of viral populations, particularly of T4-like viruses, in freshwater environments.     

A comparison of the phytosociology and dynamics of three floodplain (Várzea) forests of known ages, Rio Jurua, western Brazilian Amazon

CAMPBELL, D. G., STONE, J. L. & ROSAS Jr, A., 1992. A comparison of the phytosociology and dynamics of three floodplain (Várzea) forests of known ages, Rio Juruá, western Brazilian Amazon. An unusual historic accident has resulted in three adjacent inundated (vórzea) forests of known ages (50 years old, 14–50 years old, and 14 years old), on the margin of the Rio Juruá, near the village of Rodrigues Alves in western Acre, Brazilian Amazon. One-hectare quantitative inventories (500 × 20 m) were conducted on each of the three forests. Physical characteristics of the plots, including soil particle size, soil cation levels, level of inundation and rate of soil deposition were measured. Plot 1, steeply sloping and ecotonal between várzea and terra firme, was infrequently flooded, with a mean high water mark of 0.0. Plot 2, on slightly undulating terrain, had a mean high water mark of 1.16 m. Plot 3 was level and deeply-flooded, with a mean high water mark of 4.00 m. All trees ≥ 10 cm diameter at breast height (dbh) were mapped, measured and identified to species. Plots 1, 2 and 3 contained 523, 420 and 777 trees, 106, 73 and 20 species, Shannon diversity indices of 3.60, 3.51 and 1.82, and stand basal areas of 25.46 m², 27.01 m² and 25.72 m², respectively. Alchomea triplinervia was the superior competitor on species-rich plot 1; Annona sp. strongly dominated in the limiting conditions of plot 3. On plot 2, no single species was able to achieve dominance. For the 25 species with N≥ 10, habitat specialization as a function of the level of annual inundation was demonstrated, and for five of these species that occurred on plot 1, further refinement of niche as a function of gradient was demonstrated. One-year mortality in plots 1, 2 and 3, was 1.99%, 1.56% and 1.70%, respectively. In Plot 3, 77% of the mortalities were trees that had died standing, vs 40% and 43% in plots 1 and 2.     

Diversity and Spatial Distribution of Prokaryotic Communities Along A Sediment Vertical Profile of A Deep-Sea Mud Volcano

We investigated the top 30-cm sediment prokaryotic community structure in 5-cm spatial resolution, at an active site of the Amsterdam mud volcano, East Mediterranean Sea, based on the 16S rRNA gene diversity. A total of 339 and 526 sequences were retrieved, corresponding to 25 and 213 unique (≥98% similarity) phylotypes of Archaea and Bacteria, respectively, in all depths. The Shannon–Wiener diversity index H was higher for Bacteria (1.92–4.03) than for Archaea (0.99–1.91) and varied differently between the two groups. Archaea were dominated by anaerobic methanotrophs ANME-1, -2 and -3 groups and were related to phylotypes involved in anaerobic oxidation of methane from similar habitats. The much more complex Bacteria community consisted of 20 phylogenetic groups at the phylum/candidate division level. Proteobacteria, in particular δ-Proteobacteria, was the dominant group. In most sediment layers, the dominant phylotypes of both the Archaea and Bacteria communities were found in neighbouring layers, suggesting some overlap in species richness. The similarity of certain prokaryotic communities was also depicted by using four different similarity indices. The direct comparison of the retrieved phylotypes with those from the Kazan mud volcano of the same field revealed that 40.0% of the Archaea and 16.9% of the Bacteria phylotypes are common between the two systems. The majority of these phylotypes are closely related to phylotypes originating from other mud volcanoes, implying a degree of endemicity in these systems.     

Characterization of methanogenic and prokaryotic assemblages based on mcrA and 16S rRNA gene diversity in sediments of the Kazan mud volcano (Mediterranean Sea)

The diversity of the methyl‐coenzyme reductase A (mcrA) and 16S rRNA genes was investigated in gas hydrate containing sediment from the Kazan mud volcano, eastern Mediterranean Sea. mcrA was detected only at 15 and 20 cm below seafloor (cmbsf) from a 40‐cm long push core, while based on chemical profiles of methane, sulfate, and sulfide, possible anaerobic oxidation of methane (AOM) depth was inferred at 12–15 cmbsf. The phylogenetic relationships of the obtained mcrA, archaeal and bacterial 16S rRNA genes, showed that all the found sequences were found in both depths and at similar relative abundances. mcrA diversity was low. All sequences were related to the Methanosarcinales, with the most dominant (77.2%) sequences falling in group mcrA‐e. The 16S rRNA‐based archaeal diversity also revealed low diversity and clear dominance (72.8% of all archaeal phylotypes) of the Methanosarcinales and, in particular, ANME‐2c. Bacteria showed higher diversity but 83.2% of the retrieved phylotypes from both sediment layers belonged to the δ‐Proteobacteria. These phylotypes fell in the SEEP‐SRB1 putative AOM group. In addition, the rest of the less abundant phylotypes were related to yet‐uncultivated representatives of the Actinobacteria, Spirochaetales, and candidate divisions OP11 and WS3 from gas hydrate‐bearing habitats. These phylotype patterns indicate that AOM is occurring in the 15 and 20 cmbsf sediment layers.     

Continuous enrichment culturing of thermophiles under sulfate and nitrate-reducing conditions and at deep-sea hydrostatic pressures

A continuous culture bioreactor was developed to enrich for nitrate and sulfate reducing thermophiles under in situ deep-sea pressures. The ultimate objective of this experimental design was to be able to study microbial activities at chemical and physical conditions relevant to seafloor hydrothermal vents. Sulfide, sulfate and oxide minerals from sampled seafloor vent-chimney structures [East Pacific Rise (9°46′N)] served as source mineral and microbial inoculum for enrichment culturing using nitrate and sulfate-enriched media at 70 and 90°C and 250 bars. Changes in microbial diversity during the continuous reaction flow were monitored using denaturing gradient gel electrophoresis (DGGE) of PCR amplified 16S rRNA gene fragments. Time series changes in fluid chemistry were also monitored throughout the experiment to assess the feedback between mineral–fluid reaction and metabolic processes. Data indicate a shift from the dominance of epsilon Proteobacteria in the initial inoculum to the several Aquificales-like phylotypes in nitrate-reducing enrichment media and Thermodesulfobacteriales in the sulfate-reducing enrichment media. Methanogens were detected in the original sulfide sample and grew in selected sulfate-enriched experiments. Microbial interactions with anhydrite and pyrrhotite in the chimney material resulted in measurable changes in fluid chemistry despite a fluid residence time only 75 min in the reactor. Changes in temperature rather than source material resulted in greater differences in microbial enrichments and mediated geochemical reactions.     

Highly diverse community structure in a remote central Tibetan geothermal spring does not display monotonic variation to thermal stress

We report an assessment of whole-community diversity for an extremely isolated geothermal location with considerable phylogenetic and phylogeographic novelty. We further demonstrate, using multiple statistical analyses of sequence data, that the response of community diversity is not monotonic to thermal stress along a gradient of 52-83 degrees C. A combination of domain- and division-specific PCR was used to obtain a broad spectrum of community phylotypes, which were resolved by denaturing gradient gel electrophoresis. Among 58 sequences obtained from microbial mats and streamers, some 95% suggest novel archaeal and bacterial diversity at the species level or higher. Moreover, new phylogeographic and thermally defined lineages among the Cyanobacteria, Chloroflexi, Eubacterium and Thermus are identified. Shannon-Wiener diversity estimates suggest that mats at 63 degrees C supported highest diversity, but when alternate models were applied [Average Taxonomic Distinctness (AvTD) and Variation in Taxonomic Distinctness (VarTD)] that also take into account the phylogenetic relationships between phylotypes, it is evident that greatest taxonomic diversity (AvTD) occurred in streamers at 65-70 degrees C, whereas greatest phylogenetic distance between taxa (VarTD) occurred in streamers of 83 degrees C. All models demonstrated that diversity is not related to thermal stress in a linear fashion.     

Contrasting patterns of genetic structure and phylogeography in the marine agarophytes Gelidiophycus divaricatus and G. freshwateri (Gelidiales,Rhodophyta) from East Asia

The evolutionary and population demographic history of marine red algae in East Asia is poorly understood. Here, we reconstructed the phylogeographies of two upper intertidal species endemic to East Asia, Gelidiophycus divaricatus and G. freshwateri. Phylogenetic and phylogeographic inferences of 393 mitochondrial cox1, 128 plastid rbcL, and 342 nuclear ITS2 sequences were complemented with ecological niche models. Gelidiophycus divaricatus, a southern species adapted to warm water, is characterized by a high genetic diversity and a strong geographical population structure, characteristic of stable population sizes and sudden reduction to recent expansion. In contrast, G. freshwateri, a northern species adapted to cold temperate conditions, is genetically relatively homogeneous with a shallow population structure resulting from steady population growth and recent equilibrium. The overlap zone of the two species roughly matches summer and winter isotherms, indicating that surface seawater temperature is a key feature influencing species range. Unidirectional genetic introgression was detected at two sites on Jeju Island where G. divaricatus was rare while G. freshwateri was common, suggesting the occurrence of asymmetric natural hybrids, a rarely reported event for rhodophytes. Our results illustrate that Quaternary climate oscillations have left strong imprints on the current day genetic structure and highlight the importance of seawater temperature and sea level change in driving speciation in upper intertidal seaweed species.     

Seasonal and spatial diversity of microbial communities in marine sediments of the South China Sea

This study was conducted to characterize the diversity of microbial communities in marine sediments of the South China Sea by means of 16S rRNA gene clone libraries. The results revealed that the sediment samples collected in summer harboured a more diverse microbial community than that collected in winter, Deltaproteobacteria dominated 16S rRNA gene clone libraries from both seasons, followed by Gammaproteobacteria, Acidobacteria, Nitrospirae, Planctomycetes, Firmicutes. Archaea phylotypes were also found. The majority of clone sequences shared greatest similarity to uncultured organisms, mainly from hydrothermal sediments and cold seep sediments. In addition, the sedimentary microbial communities in the coastal sea appears to be much more diverse than that of the open sea. A spatial pattern in the sediment samples was observed that the sediment samples collected from the coastal sea and the open sea clustered separately, a novel microbial community dominated the open sea. The data indicate that changes in environmental conditions are accompanied by significant variations in diversity of microbial communities at the South China Sea.     

Abdominal setae and midgut bacteria of the mudshrimp Pestarella tyrrhena

We investigated the diversity of the bacterial 16S rRNA genes occurring on the abdominal setal tufts and in the emptied midgut of the marine mudshrimp Pestarella tyrrhena (Decapoda: Thalassinidea). There were no dominant phylotypes on the setal tufts. The majority of the phylotypes belonged to the phylum Bacteroidetes, frequently occurring in the water column. The rest of the phylotypes were related to anoxygenic photosynthetic α-Proteobacteria and to Actinobacteria. This bacterial profile seems more of a marine assemblage rather than a specific one suggesting that no specific microbial process can be inferred on the setal tufts. In the emptied midgut, 64 clones were attributed to 16 unique phylotypes with the majority (40.6%) belonging to the γ-Proteobacteria, specifically to the genus Vibrio, a marine group with known symbionts of decapods. The next most abundant group was the ɛ-Proteobacteria (28.1%), with members as likely symbionts related to the processes involving redox reactions occurring in the midgut. In addition, phylotypes related to the Spirochaetes (10.9%) were also present, with relatives capable of symbiosis conducting a nitrite associated metabolism. Entomoplasmatales, Bacteroidetes and Actinobacteria related phylotypes were also found. These results indicate a specific bacterial community dominated by putative symbiotic Bacteria within the P. tyrrhena’s midgut.     

Analysis of the Rumen Bacterial Diversity under two Different Diet Conditions using Denaturing Gradient Gel Electrophoresis,Random Sequencing,and Statistical Ecology Approaches

Bacterial community structure and diversity in the rumen of steers in conditions of hay and corn diets was assessed by in vitro retrieval and analysis of the variable region (V3) of 16S rDNA. Two types of libraries were generated in this study: DGGE libraries, which further were analysed by excising, reamplification, and sequencing, and random shotgun sequence libraries. Phylogenetic and sequence similarity analyses of the resultant 68 clone sequences in DGGE libraries revealed the presence of 42 operational taxonomic units (OTUs) or phylotypes defined as having more than 97% of sequence similarity. One hundred and thirty four clone sequences in shotgun libraries were clustered into 72 phylotypes. The phylotype similarity, diversity, richness, and evenness in these libraries were estimated using a variety of diversity indices. In relation to diet, the corn-fed animals displayed more diverse and rich bacterial populations, which were mostly contributed by CFB-related phylotypes. Proteobacteria were also numerically prevalent on this diet (27%) but were represented by a few phylotypes thus diminishing the overall diversity and species richness values. On hay diet, the principal contributors to general diversity and species richness appeared to be low-G + C gram-positives. Although the ruminal Treponemaes were encountered only in hay-fed animals, their impact on species diversity on hay diet was low because of the limited number of phylotypes.     

Distribution and Diversity of Aerobic Carbon Monoxide-Oxidizing Bacteria in Geothermal Springs of China,the Philippines,and the United States

Accumulating genomic evidence suggests that a variety of thermophilic bacteria contain cox operons and may be capable of aerobic carbon monoxide (CO) oxidation. However, little is known about the distribution and diversity of the cox-encoding (COXE) bacteria in natural geothermal environments. In this study, we examined coxL gene (encoding the large subunit of carbon monoxide dehydrogenase: CoxL) sequences retrieved from the sediments of 25 geothermal sites located in the Qinghai-Tibetan Plateau (QTP) and Yunnan Province (YP) of China, the Bacon-Manito Geothermal Production Field (BGPF) of the Philippines, and the Great Basin of the United States (USGB). Temperature and pH ranges of the studied hot springs were 22.1 to 90.8°C and 2.7 to 9.4, respectively. Phylogenetic analyses showed that most CoxL sequences were closely related to the classes Actinobacteria, Deinococci, Ktedonobacteria, Thermomicrobia, and Clostridia, and hot springs from different regions hosted different COXE communities. In addition, these hot springs harbored some COXE bacteria that were phylogenetically distinct from those inhabiting nongeothermal ecosystems. This study revealed no significant correlation between temperature or pH and the composition or diversity of COXE communities at the global scale. However, within a given region, temperature was correlated with the COXE bacterial community composition.     

Effects of the antibiotic growth promoters flavomycin and florfenicol on the autochthonous intestinal microbiota of hybrid tilapia (Oreochromis niloticus ♀ × O. aureus ♂)

The 16S rDNA PCR-DGGE and rpoB quantitative PCR (RQ-PCR) techniques were used to evaluate the effects of dietary flavomycin and florfenicol on the autochthonous intestinal microbiota of hybrid tilapia. The fish were fed four diets: control, dietary flavomycin, florfenicol and their combination. After 8 weeks of feeding, 6 fish from each cage were randomly chosen for the analysis. The total number of intestinal bacteria was determined by RQ-PCR. The results showed that dietary antibiotics significantly influenced the intestinal microbiota and dramatically reduced the intensity of total intestinal bacterial counts. The intensity of some phylotypes (EU563257, EU563262 and EU563255) were reduced to non-detectable levels by both dietary antibiotics, while supplementation of florfenicol to the diet also reduced the intensity of the phylotypes EU563242 and EU563262, uncultured Mycobacterium sp.-like, uncultured Cyanobacterium-like and uncultured Cyanobacterium (EU563246). Dietary flavomycin only reduced the OTU intensity of one phylotype, identified as a member of the phylum Fusobacteria. The antibiotic combination only reduced the phylotypes EU563242 and EU563262. Based on our results, we conclude that the reduced effect of florfenicol on intestinal microbiota was stronger than that of flavomycin, and when flavomycin and florfenicol were added in combination, the effect of florfenicol overshadowed that of flavomycin.