BackgroundBacterial communities are essential to the biogeochemical cycle in riverine ecosystems. However, little is presently known about the integrated biogeography of planktonic and sedimentary bacterial communities in large rivers.ResultsThis study provides the first spatiotemporal pattern of bacterial communities in the Yangtze River, the largest river in Asia with a catchment area of 1,800,000 km2. We find that sedimentary bacteria made larger contributions than planktonic bacteria to the bacterial diversity of the Yangzte River ecosystem with the sediment subgroup providing 98.8% of 38,906 operational taxonomic units (OTUs) observed in 280 samples of synchronous flowing water and sediment at 50 national monitoring stations covering a 4300 km reach. OTUs within the same phylum displayed uniform seasonal variations, and many phyla demonstrated autumn preference throughout the length of the river. Seasonal differences in bacterial communities were statistically significant in water, whereas bacterial communities in both water and sediment were geographically clustered according to five types of landforms: mountain, foothill, basin, foothill-mountain, and plain. Interestingly, the presence of two huge dams resulted in a drastic fall of bacterial taxa in sediment immediately downstream due to severe riverbed scouring. The integrity of the biogeography is satisfactorily interpreted by the combination of neutral and species sorting perspectives in meta-community theory for bacterial communities in flowing water and sediment.ConclusionsOur study fills a gap in understanding of bacterial communities in one of the world’s largest river and highlights the importance of both planktonic and sedimentary communities to the integrity of bacterial biogeographic patterns in a river subject to varying natural and anthropogenic impacts.Electronic supplementary materialThe online version of this article (10.1186/s40168-017-0388-x) contains supplementary material, which is available to authorized users.

Both Bacteria and Archaea might be involved in various biogeochemical processes in lacustrine sediment ecosystems. However, the factors governing the intra-lake distribution of sediment bacterial and archaeal communities in various freshwater lakes remain unclear. The present study investigated the sediment bacterial and archaeal communities in 13 freshwater lakes on the Yunnan Plateau. Quantitative PCR assay showed a large variation in bacterial and archaeal abundances. Illumina MiSeq sequencing illustrated high bacterial and archaeal diversities. Bacterial abundance was regulated by sediment total organic carbon and total nitrogen, and water depth, while nitrate nitrogen was an important determinant of bacterial diversity. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, and Verrucomicrobia were the major components of sediment bacterial communities. Proteobacteria was the largest phylum, but its major classes and their proportions varied greatly among different lakes, affected by sediment nitrate nitrogen. In addition, both Euryarchaeota and Crenarchaeota were important members in sediment archaeal communities, while unclassified Archaea usually showed the dominance.

Construction of hydroelectric dams affect river ecosystems, fish diversity, and fisheries yields. However, there are no studies assessing the combined effects on fish caused by several adjacent dams and their reservoirs, as in a 'dam cascade'. This study predicts the potential effects that a cascade of ten dams currently under construction in the upper Yangtze River in China will have on local fishes, and uses such predictions to assess the effectiveness of possible fish conservation measures. We found that the dam cascade will have serious combined effects on fishes mainly due to impoundment, habitat fragmentation and blocking, flow regime modification, and hypolimnetic discharges. The impoundments will cause loss of critical habitats for 46 endemic species. The dams will fragment the populations of 134 species and will block migration routes for 35 potamodromous fishes.Corieus guichenoti will have a high risk of extinction due to the combined effects of impoundment and blocking. Modification of the flow regime will adversely affect the recruitment of 26 species that produce drifting eggs. The start of annual spawning for 13 fishes will be postponed by more than 1 month, and fish spawning and growth opportunities will be reduced due to low water temperatures associated with hypolimnetic discharges. Combined dam effects will further reduce the likelihood of successful recruitment of some endangered species, such as Acipenser dabryanus and Psephurus gladius. Three countermeasures hold promise to mitigate the nearterm effects of the dam cascade, including preservation and rehabilitation of critical habitat, restoration of a semi-natural flow regime, and stock enhancement that respects genetic integrity. These conclusions can guide the development of protection plans for fishes in the upper Yangtze River. The approach undertaken in this study-by which the known and likely effects of present and future dams were simultaneously Electronic supplementary material The online version of this article (doi:10.1007/s11160-015-9395-9) contains supplementary material, which is available to authorized users. 123Rev Fish Biol Fisheries (2015) 25:569-585 DOI 10.1007 considered in light of the biology of the specieshighlights the usefulness of ichthyology for fish conservation.

Both planktonic and sediment bacterial assemblages are the important components of freshwater lake ecosystems. However, their spatiotemporal shift and the driving forces remain still elusive. Eutrotrophic Dianchi Lake and mesotrophic Erhai Lake are the largest two freshwater lakes on the Yunnan Plateau (southwestern China). The present study investigated the spatiotemporal shift in both planktonic and sediment bacterial populations in these two plateau freshwater lakes at different trophic status. For either lake, both water and sediment samples were collected from six sampling locations in spring and summer. Bacterioplankton community abundance in Dianchi Lake generally far outnumbered that in Erhai Lake. Sediment bacterial communities in Erhai Lake were found to have higher richness and diversity than those in Dianchi Lake. Sediments had higher bacterial community richness and diversity than waters. The change patterns for both planktonic and sediment bacterial communities were lake-specific and season-specific. Either planktonic or sediment bacterial community structure showed a distinct difference between in Dianchi Lake and in Erhai Lake, and an evident structure difference was also found between planktonic and sediment bacterial communities in either of these two lakes. Planktonic bacterial communities in both Dianchi Lake and Erhai Lake mainly included Proteobacteria (mainly Alpha-, Beta-, and Gammaproteobacteria), Bacteroidetes, Actinobacteria, Cyanobacteria, and Firmicutes, while sediment bacterial communities were mainly represented by Proteobacteria (mainly Beta- and Deltaproteobacteria), Bacteroidetes, Chlorobi, Nitrospirae, Acidobacteria, and Chloroflexi. Trophic status could play important roles in shaping both planktonic and sediment bacterial communities in freshwater lakes.

The daily periodicity of growth increment formation in sagittal otoliths of jack mackerel Trachurus japonicus was validated by marking otoliths with alizarin complexone (ALC). Analysis of otoliths of known-age juveniles confirmed that the first increment formed on day 3 after hatching, and was associated with first feeding. A total of 198 specimens, ranging from 2Á6 to 49Á2 mm in body length (notochord length or standard length) and from 7 to 78 days in age, were collected in the East China Sea and Tosa Bay, and used to examine the association between otolith morphological development and ontogenetic development. The relationship between body length (L) and otolith radius (R) was significantly described by the linear function L ¼ 2Á65 þ 0Á0425R (n ¼ 198, r 2 ¼ 0Á99, P < 0Á001), indicating that somatic growth history can be reconstructed from otolith growth patterns. The otolith was primarily spherical in the preflexion larval stage, and became elongated with notochord flexion. The first secondary primordium formed at c. 25 days, during the middle postflexion stage, and was associated with metamorphosis. By c. 42 days the sagittal otolith was adult-like in morphology, with the primary growth zone enclosed by the marginal growth zone, except in the anterior rostrum area. Thus age, growth and developmental stages were recorded in sagittal otoliths during the larval and early juvenile stages of jack mackerel. # 2005 The Fisheries Society of the British Isles

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The dominant bacterium responsible for carbon uptake from toluene in an agricultural soil was identified by stable isotope probing. Samples were amended with unlabeled toluene or labeled [ring-13 C 6 ]toluene, and DNA was extracted over time. Sequencing indicated that the organism involved belongs to the candidate phylum TM7. Microorganisms in this candidate phylum are of particular interest because although they have been found in a variety of habitats, no stable culture of any species exists, so their general metabolic capabilities are largely unknown.