Supplementary Table S2: Comparison of the relative proportions and 16S rRNA gene copy numbers of archaeal lineages based on SILVA (v. 128) between the vegetated and unvegetated sediments. Woese-3 prefers oxic environments , which was selectively enriched in vegetated sediments, possibly due to increased oxygen around the plant rhizosphere . Z. marinaleaf blades are characteristically flat and wide (2-12 mm) and can reach up to 3 meters in length (Mondragon and Mondragon, 2003) although morphology is variable and depends on environmental factors such as substrate type (Short, 1983), depth (Lee et al., 2000), temperature (Moore et al., 1996), and light and nutrient availability (Short, 1983). in shallow sublittoral sediments. There are four species of seagrass in the UK: two species of tasselweeds and two zostera species, commonly known as eelgrass. Zostera marina is a marine species and Subgenus, the Zostera Zostera. The C/N ratios of our seagrass-colonized sediments are around 10 , whereas they are generally >20 in mangroves [35, 36], where the sediment organic matter primarily consists of mangrove litter, root exudates, and other terrigenous organic debris. Sequencing and phylogenetic analysis of the resulting partial 28S rRNA gene revealed that the organism that this ASV comes from is a member of Novel Clade SW-I in the order Lobulomycetales in the phylum Chytridiomycota. However, not much is known about marine fungi and even less is known about seagrass associated fungi. The two phyla Aenigmarchaeota () and Lokiarchaeota () appeared to be minor components. According to a genomic analysis, Thermoplasmata has the capacity to degrade detrital proteins and long-chain fatty acids [32, 41]. can recover from normal grazing (Naken & Reise, 2000; Davison & Hughes, 1998). datasets have provided data to the NBN Atlas Scotland for this genus.. Browse the list of datasets and find organisations you can join if you are interested in participating in a survey for species of Zostera Linnaeus, 1753. In mangrove wetlands, pH is also an important force shaping the Bathyarchaeotal community structure . muelleri has a rounded notched leaf tip, compared with Z. nigricaulis with rounded tips.Z. In addition, latitude could be another factor governing the distribution of Woesearchaeota in the Z. marina seagrass meadow and mangroves. Learn seagrass with free interactive flashcards. The high-throughput sequencing data was available in the NCBI Sequence Read Archive under accession number PRJNA385281. All qPCR assays were based on the fluorescence intensity of the SYBR green dye and were performed to quantify archaeal 16S rRNA gene copy numbers in the sediments as previously described . Values of Shannon, Simpson, and Chao1 diversity indexes ranged from 6.39 to 6.96, 0.98 to 0.99, and 211.68 to 353.84, respectively (Table S1). Eelgrass is found on sandy Considering the significantly higher total archaeal abundance in the vegetated sediments (Figure 3), it is possible that high abundance of other archaeal subgroups supplies more byproducts for Woesearchaeota and stimulates their growth and persistence in the vegetated sites . The ecological importance of seagrass meadows is well recognized because of their burial and sequestration of organic carbon in sediments, which contributes to mitigating atmospheric CO2 increases [2, 3]. We sampled from two Z. marina beds in Bodega Bay over three time points to investigate fungal diversity within and between plants. The 16S rRNA gene copy number of each archaeal subgroup in a sample was calculated by multiplying the total archaeal quantity determined by qPCR with its corresponding proportion in that sample obtained by analyzing the high-throughput sequencing dataset  (Figure 4, Table S2). The assemblies contain 4,847,456 bp and 4,817,752 bp, respectively. Established in 1964, the IUCN Red List of Threatened Species has evolved to become the world’s most comprehensive information source on the global conservation status of animal, fungi and plant species. Common names for this species are eelgrass, seagrass, and seawrack. However, not much is known about marine fungi and even less is known about seagrass associated fungi. Enter multiple addresses on separate lines or separate them with commas. These communities are generally found in extremely sheltered embayments, marine inlets, estuaries and lagoons, with very weak tidal currents. Eelgrass is an angiosperm with true leaves, stems, and rootstocks; not an alga. Eelgrass, (genus Zostera ), genus of about 15 species of marine plants of the family Zosteraceae. In addition, the subclades Woese-3, Woese-10, Woese-13, and Woese-21 were significantly more abundant in the vegetated sediments. At Project Seagrass we wish to deliver on both of these United Nations calls to action. The rhizomes creep or ascend, and produce roots and shoots at the nodes. The data used to support the findings of this study are included within the article and the supplementary information files. Woese-2 (), Woese-9 (), and Woese-11 () were the major subclades among all samples (Figure 1(b), Table S2). It is a monoecious, predominantly annual, glabrous herb. In this study, we molecularly characterized the diazotrophic assemblages and entire bacterial community in surface sediments of a Zostera marina -colonized coastal lagoon in … Can be confused with other species in the genus Zostera.Z. Based on the evidence from enrichment experiments, Bathy-8 can grow using the refractory aromatic polymer lignin as an energy source, during which its relative proportion doubled compared to the initial stage with lignin addition . Contains 8 families total, 3 of which contain exclusively seagrasses (Cymodoceaceae, Posidoniaceae, and Zosteraceae). The pairwise differences were examined using t-tests (n = 3), and significant differences (P < 0.05) were highlighted in bold. Species Description. It is an aquatic plant native to marine environments on the coastlines of mostly northern sections of North America and Eurasia. Xu, and J.-D. Gu, “Successive transitory distribution of, P. Qian, Y. Wang, O. O. Lee et al., “Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing,”, J. G. Caporaso, K. Bittinger, F. D. Bushman, T. DeSantis, G. L. Andersen, and R. Knight, “PyNAST: a flexible tool for aligning sequences to a template alignment,”, E. Pruesse, C. Quast, K. Knittel et al., “SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB,”, R. Edgar, “Search and clustering orders of magnitude faster than BLAST,”, R. Amann, W. Ludwig, and K. H. Schleifer, “Phylogenetic identification and in situ detection of individual microbial cells without cultivation,”, M. Ortiz, A. Legatzki, J. W. Neilson et al., “Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave,”, J. Lou, L. Yang, H. Wang, L. Wu, and J. Xu, “Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification,”, C. J. Castelle, K. C. Wrighton, B. C. Thomas et al., “Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling,”, X. Today I will be blogging about a beautiful marine species called Zostera marina.  noted that most Woesearchaeota have been reported in midlatitude environments. The identified Thaumarchaeota were mainly composed of Group C3, Marine Group I (formerly referred to as Marine Group 1.1a), and Soil Crenarchaeotic Group (formerly Marine Group 1.1b) in this study (Table S2). In addition to plant proteins, many microbial proteins, representing refractory organic matter, were buried in the seagrass sediments [8, 9], and Bathy-17 might contribute to degrading this kind of substrate. Ecologists consider seagrass meadows to be foundational because they support complex food webs and provide refuge for a number of creatures. Microbes isolated from the seagrass, Zostera marina. The analysis of the genomics of Woesearchaeota indicated that this archaea group harbored nitrogen removal genes such as nirK and nosZ , suggesting that Woesearchaeota might participate in nitrogen removal processes and contribute to lower the DIN level in the vegetated sediments. 500 spp. Liang, M.-Y. The V3 region of the archaeal 16S rRNA gene was PCR amplified with adapter-modified core primers, which contained unique 12 bp bar codes and the archaeal-specific primers A344F (5-GGGGYGCASCAGGSG-3) and A519R (5-GGTDTTACCGCGGCKGCTG-3). The amplicons were gel purified and further purified with AMPure beads (Beckman Coulter, USA) and then pooled in equimolar proportions and sequenced on 318 chips with an Ion Torrent Personal Genome Machine (PGM) according to the manufacturer’s instructions (Life Technologies, USA). However, the difference in the overall archaeal community structure between these two types of sediments was not significant (ANOSIM, ). Z. marinaleaf blades are characteristically flat and wide (2-12 mm) and can reach up to 3 meters in length (Mondragon and Mondragon, 2003) although morphology is variable and depends on environmental factors such as substrate type (Short, 1983), depth (Lee et al., 2000), temperature (Moore et al., 1996), and light and nutrient availability (Short, 1983). Zostera noltei is the preferred food of the dark-bellied Brent goose (Branta bernicla). It recurrently coexists in the same sedimentary niches with Bathyarchaeota and shares the organic substrates . Includes pond weeds and relatives; consists of 15 families, 56 genera, and aprox. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The ML tree was built with the “FastTree” program and edited with the online tool iTOL (http://itol.embl.de/). 41676154, 41976115), the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao) (No. Fan and P. Xing, “The Vertical Distribution of Sediment Archaeal Community in the "Black Bloom" Disturbing Zhushan Bay of Lake Taihu,”, X. Zhang, Y.-B. Epibenthic organisms may be freely moving or sessile (permanently attached to a surface). The former is believed to be more conducive to microbial consumption. Compared with those in the unvegetated samples ( copies g-1 sediment), the absolute quantity of Woesearchaeota almost doubled in the vegetated samples ( copies g-1 wet sediment; Figure 4(a)). In addition to Bathy-6, the abundant Bathy-8 and Bathy-17 subclades showed higher proportions in vegetated sediments. Furthermore, during photosynthesis, the roots release a portion of O2 to sediments, which creates a microzone of elevated oxygen concentrations in rhizosphere sediments compared with surrounding unvegetated sediments [5, 6]. Student’s (two-tailed) -tests were performed to compare the relative proportions, absolute quantities, and alpha diversities of archaea between seagrass-vegetated and unvegetated sediments using SPSS (v. 20.0) software for Windows (SPSS, Chicago, IL, USA). Posidonia australis (strapweed), Zostera capricorni, Zostera muelleri, Heterozostera nigricaulis (all three species are commonly called eelgrass or ribbonweed), Halophila ovalis. NBN Atlas Scotland. A potential bias in our study was that two different sets of archaea-specific primers were applied for high-throughput sequencing (344F/519R) and qPCR (931F/M1100R). 1). Besides, Woesearchaeota was also usually found to be the most abundant in anaerobic nitrogen-removing wastewater treatment sludge . In this study, we investigated archaeal abundance, diversity, and composition in both vegetated and adjacent bare surface sediments of a Zostera marina meadow. Sequencing and phylogenetic analysis of the resulting partial 28S rRNA gene revealed that the organism that this ASV comes from is a member of Novel Clade SW-I in the order Lobulomycetales in the phylum Chytridiomycota. Sequencing and phylogenetic analysis of the resulting partial 28S rRNA gene revealed that the organism that this ASV comes from is a member of Novel Clade SW-I in the order Lobulomycetales in the phylum Chytridiomycota. The phylum Annelida is composed of segmented worms In the Mediterranean Sea, Annelida species have Drilonereis filum (Claparède, ). Apart from these major taxa, the minor Marine Hydrothermal Vent Group (MHVG) lineage appeared at 10 times higher abundance ( copies g-1 sediment) in vegetated sediments () (Figure 4(a)). It forms part of the Alismatales Order, which is part of the Phylum Tracheophyta that is in the Kingdom Plantae. Seagrass beds provide a variety of ecosystem services, both within and outside the bounds of the habitat itself. In the present study, the sediment cores of seagrass bed (dominated by Zostera japonica and Zostera marine) and degradation area in Swan Lake (China) were sampled; then, biogeochemical parameters were analyzed, and microbial community composition was investigated by using high-throughput sequencing of the 16S rRNA gene. In this study, we first analyzed the diversity of archaea in a Z. marina seagrass meadow and evaluated the influence of seagrass colonization on archaeal community structures and abundance through high-throughput sequencing and qPCR technologies. The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. Zostera marina. These strains were isolated from sediment surrounding the roots of the seagrass, Zostera marina , collected near the UC, Davis Bodega Marine Laboratory (Bodega Bay, California). As the second most abundant phylum, Bathyarchaeota was significantly enriched in seagrass-colonized sediments (vegetated vs. unvegetated, 26.17% vs. 15.44%) (Figure 1(a)), which was consistent with the result for mangroves [13, 16], where Bathyarchaeota generally accounted for more than 40% of the relative abundance in archaeal community, and showed significantly higher proportions in mangrove sites than the nearby mud-flat sediments . Our study expands the available knowledge of the distribution patterns and niche preferences of archaea in seagrass systems, especially for the different subclades of Woesearchaeota and Bathyarchaeota, in terms of both relative proportions and absolute quantities. To explore the phylogenetic relationships of all Woesearchaeota and Bathyarchaeota sequences with the subclades classified by Liu et al. This work highlights a need for further studies focusing on marine fungi and the potential importance of these understudied communities to the larger seagrass ecosystem. Briefly, three (V1-V3) surface (0-5 cm) sediment samples were randomly collected from the seagrass-vegetated region, and another three control (U1-U3) samples were collected from the adjacent bare (unvegetated) region in the Swan Lake lagoon (Rongcheng Bay, Yellow Sea, China) in May 2013. Thaumarchaeota adapted better to the bare sediments, while other phyla presented no heterogeneity in the two niches. To obtain a more According to sequence origins , Woese-2 and Woese-9 were only detected in anoxic environments, and Woese-2 was only observed in saline or hypersaline environments, suggesting that anoxic and saline conditions in the seagrass meadow sediments could contribute to the evolutionary diversity of Woesearchaeota. The name Zostera marina is derived from Greek roots meaning ‘sea girdle’ referring to the way the stems emerge from a sheath (Rucklehaus 1998). We then used PCR with a primer targeting unique regions of the ITS2 region of this ASV and an existing primer for the fungal 28S rRNA gene to amplify part of the 28S rRNA gene region and link it to this ASV. Seagrass wasting disease in the 1930s resulted in mass decline of seagrass Zostera marina in the Northern Atlantic Ocean. How this seagrass colonization-induced spatial heterogeneity affects archaeal community structure and abundance remains unclear. Here, we present the archaeal community diversity and distribution patterns in a Z. marina seagrass meadow for the first time. Woese-20 presented an opposite pattern that was selectively enriched in the bare sediments. 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