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2015;49:7597–605. Cotner JB Jr, Wetzel RG. 2003;300:958–61. In: Fontaine, T.D., Bartell SM, editor. Estuar Coast Shelf Sci. Biodiversity, biogeography and conservation of diatoms. CAS Comparing with the spatial dispersal process, the environmental selection process was the major driver for diatom biogeography, which could be further interpreted in terms of photosynthetically active radiation, hydraulic slope, nutrients, and human activities (the Three Gorges Dam and the Xiluodu Dam). Review of basic definitions of nekton, benthos, and plankton with examples. J Yangtze River Sci Res Inst. 4c). 2016;32:3246–51. 2008;596:173–85. For example, Liu et al. Canonical correspondence analysis (CCA) showed significant correlations between diatom communities and specific environmental and spatial factors such as water temperature, pH, suspended solids, and PCNM-1 (Additional file 1: Table S3). CAS Science. Planktonic diatoms exhibited the highest alpha-diversity (Chao1 and Shannon indices) and benthic diatoms the lowest richness (Chao1) in the plateau (Additional file 1: Figure S3). 2010;20:803–17. PubMed Central Significant differences in abundance of benthic diatoms upstream and downstream of Xiluodu Dam (a) and Three Gorges Dam (b). Despite their ecological significance, little is known about their seasonal co-occurrence patterns and the ecological processes that drive them. Anaerobic ammonia oxidation in a fertilized paddy soil. Google Scholar. Ecol Indic. Unlike nekton and planktons, benthos linked to the ocean floor. Planktonic and benthic diatoms demonstrate spatial dissimilarities in different types of landforms corresponding to varying soil property, temperature, altitude, light, and nutrients. The terms ‘Benthic’ and ‘Pelagic’ are both derived from Greek words, which mean ‘depth of the sea’ and ‘open sea’, respectively. Mann DG, Droop SJM. Cookies policy. Referring to a previous study on landform types in the Yangtze , planktonic diatoms were represented by Cymbella, Asterionella, Stephanodiscus, Melosira, Cyclotella, and Conticribra in the plateau, mountain, foothill, basin, foothill-mountain, and plain regions, respectively, while benthic diatoms were abundant by Cymbella, Navicula, Melosira, Conticribra, Cyclotella, and Surirella, respectively, in the corresponding regions (Fig. In riverine ecosystems, both planktonic and benthic algae are the important components of primary producers. Both planktonic and benthic species are sensitive to changes in food availability as well as physical environmental parameters, such as salinity and temperature. Moniz MBJ, Kaczmarska I. Barcoding of diatoms: nuclear encoded ITS revisited. Amplification of the V4 region of the 18S rDNA was performed by polymerase chain reaction (PCR) using barcoded primers DIV4for (5′-GCGGTAATTCCAGCTCCAATAG-3′) and DIV4rev3 (5′-CTCTGACAATGGAATACGAATA-3′) , where barcode is an eight-base sequence unique to each sample. Tantanasarit C, Englande AJ, Babel S. Nitrogen, phosphorus and silicon uptake kinetics by marine diatom Chaetoceros calcitrans under high nutrient concentrations. Gapped BLAST and PSI-BLAST: anew generation of protein database search programs. 1998;281:237–40. Please add askdifference.com to your ad blocking whitelist or disable your adblocking software. Both the planktonic bacterial community (PBC) and benthic bacterial community (BBC) are important for biogeochemical processes in freshwater lakes. Buma AGJ, Engelen AH, Gieskes WWC. 2013;69:47–57. 2012;406:01. Integrated biogeography of planktonic and sedimentary bacterial communities in the Yangtze River. Dili Xuebao/Acta Geogr Sin. Furthermore, one-way ANOVA analysis also revealed significant difference in environmental variables (pH (P = 0.003), NH4-N (P < 0.001), TN (P < 0.001), and TN:TP (P = 0.01)) for sediment samples immediately before and after the Three Gorges Dam. Inner circular diagram shows relative abundance of different diatom genus in six sample types. 2018;11:27–37. Article Variation partitioning of benthic diatom community matrices: effects of multiple variables on benthic diatom communities in an Austral temperate river system. Typical benthic diatoms, such as Pinnularia, Paralia, and Aulacoseira, experienced considerable reduction in relative abundance downstream of the Three Gorges Dam and the Xiluodu Dam, two of the world’s largest dams. We extended these guilds by adding supplemented classifications used in other studies [79, 80]. Zhang W, Yuan J, Han J, Huang C, Li M. Impact of the Three Gorges Dam on sediment deposition and erosion in the middle Yangtze River: a case study of the Shashi Reach. Chen et al. Ecol Monogr. First let's learn how to recognize planktonic vs benthic diatom, and try out our skills. All of the authors contributed to interpretation of the findings and approved the final version of the manuscript. 2012;13:222–31. A mesoscale iron enrichment in the western subarctic pacific induces a large centric diatom bloom. Figure S10. More than ⅔ of the Earth’s surface is made up of water. Planktonic diatoms were dominated by Cyclotella (average relative abundance: 17.66%), Stephanodiscus (12.81%), Pinnularia (7.53%), Paralia (7.34%), and Skeletonema (4.90%), whereas benthic diatoms were dominated by Navicula (13.12%), Cyclotella (10.33%), Pinnularia (10.12%), Surirella (7.10%), and Stephanodiscus (6.53%). Benthic Foraminifera Planktonic Foraminifera Oxygen Isotope Stage Planktic Foraminifera Marine Micropaleontology These keywords were added by machine and not by the authors. Floating in the open sea rather than living on the seafloor. Although the most ideal sampling should be the synchronous monitoring in both plateau and non-plateau areas in the same year, the above remedial sampling is helpful considering insignificant inter-annual variations of water quality, riverine habitat, and aquatic organism in the plateau in recent years [66, 67]. This is because both proxies are preserved in planktonic and benthic foraminiferal shells and show chemical contrasts between the surface and deep oceans in response to the biological pump, yet there are differences in behaviour (in particular the effect of air-sea exchange on δ 13 C) which leads to potentially revealing discrepancies in their palaeoceanographic distributions (e.g., Boyle 1988, … LEfSe cladogram of planktonic (a) and benthic (b) diatom communities for the three channel slope regions. 3c). In the Yangtze River, the planktonic diatoms such as Asterionella formosa, Diatoma vulgare, Lindavia viaradiosa, Gomphonema pumilum, and Thalassiosira nordenskioeldii were significantly strongly associated with dissolved carbon dioxide (pCO2, see the “Methods” section) (Spearman r > 0.3, P < 0.05), while the benthic diatoms Asterionella formosa, Encyonema prostratum, Eucocconeis laevis, Fistulifera saprophila, and Nitzschia sigmoidea were highly correlated with pCO2 (Additional file 1: Figure S7). Nutrient condition, represented by the total nitrogen to total phosphorus ratio (TN:TP), was considered as an indicator of ecosystem to support for algae biomass . PubMed Morphological analysis requires extensive taxonomic expertise and may exhibit shortcomings in characterizing specific diatoms in rivers . Alpha diversity index per diatom community for each sample type. 2009;75:7537–41. Diatom communities in the plateau region were quite different from those in the non-plateau region of the Yangtze River, as evidenced by the higher percentage of top indicator species in water-plateau and sediment-plateau samples (Additional file 1: Figure S9). Contribution of epilithic diatoms to benthic-pelagic coupling in a temperate river. Cite this article. Figure S8. Proportion of indicator diatoms in each sample type obtained using indicator taxa analysis at Class (a), Order (b), Family (c), and Genus (d) levels. Liu T, Zhang AN, Wang J, Liu S, Jiang X, Dang C, et al. In short, 75 mL of river water was collected in a 100 mL polypropylene syringe. This disperse ability is a key adaptation of benthic marine invertebrates. 2a).  calculated and spatialized PAR using data simulation method  based on three climatic datasets, i.e., daily sunshine duration data at 740 weather stations across China for 1961–2007 and global radiation data at 122 radiation stations across China for 1961–2000 from China Meteorological Administration, and PAR observatory data at 36 field stations across China for 2004–2007 from Chinese Ecosystem Research Network. INTRODUCTION. PubMed Google Scholar. A motile ecological guild has the ability to move fast and choose the best microhabitat in a given circumstance. Moreover, Chen et al. Diatoms were divided into four ecological guilds according to their biological traits, including low-profile, high-profile, motile, and planktic guilds in terms of different responses to nutrients and dynamic disturbances [31,32,33] (see “Ecological guilds classification” section). 2007;86:171–8. Environmental monitoring: inferring the diatom index from next-generation sequencing data. PubMed Diatoms are ubiquitous and diverse species of single-celled, eukaryotic, photosynthetic microorganisms , and are often the dominant primary producers in marine and freshwater ecosystems . 402-409. Sims PA, Mann DG, Medlin LK. The LEfSe biomarker detection was performed in QIIME  using the logarithmic LDA threshold > 4 and the statistical parameters of P < 0.05. Although planktonic and benthic communities of the three lakes were mainly composed of the same groups of uncultured archaea, differences in their relative composition were large enough to segregate communities from both habitats in a 2D space with low stress (0.12, Fig. 1980;37:130–7. Regardless of the diatoms in an unspecified ecological guild, planktonic diatoms were dominant in the planktic guild. The steep bathymetry … First, it has been reported that sufficient PAR drives the growth and production of diatoms , but excess PAR can affect various cellular processes and reduce the growth or viability of diatoms . Wang, J., Liu, Q., Zhao, X. et al. Environ Sci Technol. Therefore, diatoms in such ecosystems may be remarkably dissimilar either in phylogenetic composition or biogeographic distribution [5, 6]. A completed description on biogeographic pattern over a large river requires to identify the difference in diatom compositions among different types of samples and their spatiotemporal heterogeneity. Dissolved carbon dioxide (pCO2) in water was measured using a headspace equilibration technique . Sequences of diatom 18S rDNA were quality-filtered using QIIME  as follows: (i) minimum sequence length of 300 bp, and minimum threshold quality score of Q20; (ii) maximum mismatches of 2 for matching the primer; any reads with ambiguous bases were removed; and (iii) merged pair-ended sequences that overlapped longer than 10 bp into a single sequence. Article Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL, et al. Solar radiation with wavelengths (400–700 nm), called photosynthetically active radiation (PAR), is able to be utilized by plants and algae through photosynthesis to convert light energy into biomass . PCR mixtures (20 μL volume) were prepared in triplicate contained 2 μL of 10 × buffer, 2 μL of 2.5 mM dNTPs, 0.8 μL of each primer (5 μM), 0.2 μL of rTaq polymerase, 0.2 μL of BSA, and 1 μL of 10 ng DNA sample. Biogeographical distribution of diatoms at class level throughout the mainstream of the Yangtze for: (a) water-spring, (b) water-autumn, (c) sediment-spring, and (d) sediment-autumn samples. Field investigation on river hydrochemical characteristics and larval and juvenile fish in the source region of the Yangtze River. Kelly MG. Use of the trophic diatom index to monitor eutrophication in rivers. Spatially, the annual-averaged PAR exhibits four stages along the Yangtze River , i.e., the highest in the upper reach located in Qinghai-Tibet Plateau region (above 32 mol m−2 d−1), the higher in the reach located in the Hengduan Mountains, the lowest in the reach located in the Sichuan Basin (below 23 mol m− d−1), and the moderate in the lower reach (Fig. b Metabarcoding analysis provides insights into biogeographic pattern of diatoms along the mainstream of the Yangtze River, represented by the spatial distribution of Shannon diversity. Relationships between Shannon diversity and TN:TP for water-spring (a), water-autumn (b), sediment-spring (c), and sediment-autumn (d) samples. Jäger CG, Diehl S. Resource competition across habitat boundaries: asymmetric interactions between benthic and pelagic producers. Depauw FA, Rogato A, D’Alcalá MR, Falciatore A. As a deterministic process, environmental selection played a critical role in the biogeography of planktonic and benthic diatoms. J Environ Sci (China). Google Scholar. Second, the richness of planktonic diatoms appeared to fluctuate with PAR, whereas the richness of benthic diatoms tended to change with … Then, the selected OTUs were checked by means of the phylogenetic tree, and only OTUs with correct taxonomical assignment were retained for further analysis. Article Spatial factors contribute to benthic diatom structure in streams across spatial scales: considerations for biomonitoring. 3c, see the “Photosynthetically active radiation (PAR) divisions” section). Zhu et al. QIIME allows analysis of high-throughput community sequencing data. CAS Air bubbles drawn in with the sample were eliminated by tapping and draining water while the syringe is pointing upwards. In this study, we aimed to investigate the ecological associations among bacterial taxa and assembly … The influence of organisms on the composition of seawater. Obvious difference in species composition was observed in planktonic and benthic diatoms. Foraminiferal assemblages from the Bifurcatus Zone (Oxfordian, Upper Jurassic) are studied in the Navalperal section (Betic Cordillera, southern Spain). Mitrovic SM, Chessman BC, Davie A, Avery EL, Ryan N. Development of blooms of Cyclotella meneghiniana and Nitzschia spp. This process is experimental and the keywords may be updated as the learning algorithm improves. © 2020 BioMed Central Ltd unless otherwise stated. We need money to operate the site, and almost all of it comes from our online advertising. Soininen et al. Figure S2. Diatoms come in all shapes and sizes. J Mar Syst. Figure S7. For relatively oligotrophic rivers like the Yangtze River, it appeared that TN was more important than TP as limiting nutrients to planktonic and benthic community variability (Additional file 1: Table S3). It can be further confirmed, that is, contrary to the planktonic diatoms, the average richness of benthic diatoms immediately downstream of Three Gorges Dam is significantly lower than that of upstream reaches. predominated in diatom communities in Lake Kasumigaura, Japan . Orange and blue circles display the average alpha-diversity (Chao1) of planktonic and benthic diatoms respectively in different photosynthetically active radiation (PAR) regions, and their sizes correspond to the Chao1 index (c). Planktonic (adjective) Floating in the open sea rather than living on the seafloor. ISME J. Front. Zhu X, He H, Liu M, Yu G, Sun X, Gao Y. Spatio-temporal variation of photosynthetically active radiation in China in recent 50 years. Liu et al. The lowest value of TN:TP in water samples was obtained in river reaches receiving large inflow from the Min River, and the highest value was obtained in both water and sediment samples near river estuary. Kheiri S, Solak CN, Edlund MB, Spaulding S, Nejadsattari T, Asri Y, et al. Exploring the molecular basis of responses to light in marine diatoms. Planktonic GPP increased with nutrients status, whereas benthic GPP decreased. In marine ecosystems, diatoms were abundant in nutrient-rich coastal zones particularly at high latitudes. 4, pp. Google Scholar. With the development of high-throughput sequencing (HTS) technology, DNA metabarcoding has become a rapid, accurate, and reliable method for diatom detection . planktonic | nektonic | Planktonic is a see also of nektonic. • Pelagic food webs are powered by photosynthesis whereas benthic communities are normally powered by detritus drifted from the upper layers. In the Yangtze River, environmental selection appears to explain at least three times more of the community variance (either in planktonic or benthic diatoms) than spatial dispersal process (Additional file 1: Figure S12), which is in line with previous findings on planktonic  and benthic diatoms  in streams and rivers. 2014;84:287–302. For the Yangtze River, one of the most prominent impacts on its ecology arises from the construction and operation of large dams. Photosynthetically active radiation (PAR, 400–700 nm) is utilized by diatoms to synthesize biomass through photosynthesis . Significant distance-decay in diatom similarity was observed along the geographical distance (Additional file 1: Figure S11), with a greater slope of the curve for water (slope = − 0.042) than for sediment (slope = − 0.038) using least squares linear regression. Genome Biol. 2005;32:1–4. Kunz et al  reported that sediment, carbon, nitrogen, and phosphorus were trapped by the reservoir immediately upstream of the Itezhi-Tezhi Dam, increasing the N:P ratio downstream of the dam. Benthic foraminifera include two major types of foraminifera. Furthermore, it not only weakens the competitive interactions for light and nutrients between benthic and planktonic diatoms, but also reduces their migration rate. Liu J, Soininen J, Han B-P, Declerck SAJ. For example, Centis et al. Introducing MOTHUR: open-source, platform-independent, community-supported software for describing and comparing microbial communities. All sequencing reads were classified into 3947 operational taxonomic units (OTUs) at a 97% similarity threshold, with 3144 OTUs well matching 454 diatom species in our reference database. Kireta AR, Reavie ED, Sgro GV, Angradi TR, Bolgrien DW, Hill BH, et al. The rate of distance-decay of diatom communities was calculated as the slope of ordinary least-squares regression line fitted to the relationship between geographic distance and community similarity. • No photosynthetic organism can be found in the benthic region; it is dominated by detritivores and scavengers. Meanwhile, Navicula, Pinnularia, and Cyclotella became the dominant genera, represented 14.4, 9.1, and 6.9% of total sequences, respectively, in sediment samples, in which Navicula was dominant in either sediment-plateau (17.1%), sediment-autumn (13.1%), or sediment-spring samples (13.2%). Using the indicator species analysis, the diatoms that were responsible for the observed community differences among the six types of samples could be well identified (Additional file 1: Table S1). The spatial distribution of TN:TP in water and sediment samples varied in different sampling stations. Vannote RL, Minshall GW, Cummins KW, Sedell JR, Cushing CE. Part of Berthon V, Bouchez A, Rimet F. Using diatom life-forms and ecological guilds to assess organic pollution and trophic level in rivers: a case study of rivers in south-eastern France. Molecular biogeography of planktonic and benthic diatoms in the Yangtze River. Planktonic and periphytic diatoms as indicators of stress on great rivers of the United States: testing water quality and disturbance models. Although Kireta et al. 4a, b). Insights into global diatom distribution and diversity in the world’s ocean. Necchi JR O, editor. Third, sequence alignment was performed by Mafft (ver 7.310) , then the sequences were analyzed to construct an approximately-maximum-likelihood phylogenetic tree using FastTree (ver 2.1.10) , and any incorrect reads discarded. Nutrient level (TN:TP) had different effects on the diversity and variation of planktonic and benthic diatoms. Second, as a primary driver of stream power that shapes the spatial distribution of diatoms, the channel slope not only affects competitive and succession processes among species but also alters nutritional utilization strategies and hence the production and growth of diatoms , leading to diatoms preferring to different flow conditions . 2019;665:171–80. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Mar Ecol Prog Ser. (2016). 2011;47:W12531. Article Afterwards, sample libraries were pooled in equimolar amounts and sequenced on Illumina MiSeq 2 × 250 PE platform (Majorbio Company, Shanghai, China). Phytoplankton are the Planktonic vs benthic ecology plankton or the producers. First, we extracted all diatom sequences of 18S rRNA reads from GenBank (http://www.ncbi.nlm.nih.gov/). Forams are lumped into two groups: benthic foraminifera that live on the sea floor, and planktonic foraminifera that live suspended in the water column. Huang Z, Liu Y, Zhao W, Zhao L. Discussion on recent spatial-temporal distribution of water quality in Changjiang River source area. UCHIME was used to remove chimeric sequences and UPARSE was used to cluster operational taxonomic units (OTUs) with 97% similarity cutoff . Agric For Meteorol. 2016;113:E1516–25. Taxonomic compositions of riverine diatoms in the Yangtze River are markedly different from those in lakes  and oceans  because of the distinct differences in salinity and hydraulic conditions. Planktonic vs. Benthic. Science. Malviya S, Scalco E, Audic S, Vincent F, Veluchamy A, Poulain J, et al.  also suggested that the spatial distribution of annual-averaged PAR is complex and inhomogeneous across China, using calculated PAR spatial data for the period 1961–2007 provided by China Meteorological Administration. Benthic (bottom-dwelling) foraminifera also use their pseudopodia for locomotion. Hydrobiologia. 3), indicating that diatoms possess diverse light-regulatory mechanisms and adaptive responses . Accurate identification of diatoms depends on the reliability of the methods used. Mol Ecol Resour. Science. High flow downstream of dams has caused severe erosion of the riverbed and led to coarsening of bed materials . Heino J, Bini LM, Karjalainen SM, Mykrä H, Soininen J, Vieira LCG, et al. 4A). Geomorphology. A low-profile guild is defined as having high reproduction rate, low nutrient and light availability, and slow-moving diatoms. After equilibration, the headspace gas was immediately transferred to a pre-vacuum glass storage vial equipped with chlorobutyl septa. The dominant genera were found to be Cyclotella, Stephanodiscus, Pinnularia, and Paralia, represented 12.2, 8.6, 7.3, and 6.6% of total sequences, respectively, in water samples. Peters F, Arin L, Marrasé C, Berdalet E, Sala MM. Upstream Freshwater and Terrestrial Sources Are Differentially Reflected in the Bacterial Community Structure along a Small Arctic River and Its Estuary. 2, Additional file 1: Figure S4 and Figure S9). Kunz MJ, Wüest A, Wehrli B, Landert J, Senn DB. Consequently, preferred planktonic and benthic diatom species in different PAR regions were identified (Fig. Downstream hydrologic and geomorphic effects of large dams on American rivers. In the mountainous reaches (stations 1~2), the river channel slope can be higher than 400 × 10−5. Various DNA barcoding studies have been successfully conducted, based on different maker genes, including COI , ITS , and 18S rDNA [9, 12]. Soininen J. Determinants of benthic diatom community structure in boreal streams: the role of environmental and spatial factors at different scales. In order of abundance, the most common riverine diatoms in water and sediment of the Yangtze River were Cyclotella, Navicula, Pinnularia, Stephanodiscus, and Cymbella genera. PubMed Central Planktonic foraminifera account for only around 50 species of 10,000 species around today. Numbers of Indicator species and Top Indicator species across sample sites. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Except for a very few samples missed due to restrictions of steep terrain and rapid flow as described in a previous study , up to four parallel samples were collected in most cases. 2009;325:1539–41. On the other hand, seasonal differences were more evident in planktonic diatoms than benthic diatoms (Additional file 1: Figure S4-S6). The authors declare that they have no competing interests. Privacy Meanwhile, the weak seasonal difference of diatom communities in sediment may be ascribed to the majority of benthic diatoms (Additional file 1: Figure S6) that weakly respond to seasonal changes and reached a state of relative equilibrium through long-term sediment erosion and deposition processes . For sediment samples, we utilized TN and TP to calculate monitored TN:TP observed at 50 stations for 2014. Monteith reported the linear correlation between net primary production (NPP) and PAR absorbed by green foliage . Benthic (adjective) Pertaining to the benthos; living on the seafloor, as opposed to floating in the ocean. Namely, as river channel deepens, the number of planktonic diatoms from detached benthic algae and benthic diatoms from sinking planktonic algae will reduce, resulting a dominant position of primary production by planktonic algae . Diatom composition in terms of ecological guilds showed spatial dissimilarity in water and sediment samples (Additional file 1: Figure S10). Limnol Oceanogr. 2006;79:336–60. From shore to 10 m depth, autotrophic structure shifted from planktonic dominance near the mouth of the Fox River (95% planktonic) to a mix of benthic and planktonic GPP 35 km from the mouth of the Fox (∼40% benthic). LEfSe cladogram of planktonic (a) and benthic (b) diatom communities from four PAR regions. In the riverine ecosystem, diatoms of glacier origin from the Qinghai-Tibetan plateau were significantly different to those in the main body of the Yangtze River (Fig.
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