Microscopic interactions between phycosphere microbiota and host algae play crucial roles in aquatic ecosystems. Despite their significance, there is a scarcity of available genome sequences derived from the phycosphere microbiome. Here, we report the draft genome sequences of nine heterotrophic proteobacterial strains isolated from the toxic dinoflagellate Alexandrium catenella LZT09 during execution of our Phycosphere Microbiome Project. Further exploration of the genomic features of the alga-associated bacterial community will profoundly help in deeply deciphering the processes and mechanisms governing the host-microbe interactome within algal holobionts in the ocean.
ABSTRACT
Microscopic interactions between phycosphere microbiota and host algae play crucial roles in aquatic ecosystems. Despite their significance, there is a scarcity of available genome sequences derived from the phycosphere microbiome. Here, we report the draft genome sequences of nine heterotrophic proteobacterial strains isolated from the toxic dinoflagellate Alexandrium catenella LZT09 during execution of our Phycosphere Microbiome Project. Further exploration of the genomic features of the alga-associated bacterial community will profoundly help in deeply deciphering the processes and mechanisms governing the host-microbe interactome within algal holobionts in the ocean.
ANNOUNCEMENT
The phycosphere, the boundary of phytoplankton holobionts, is a unique microscopic niche for host-microbe interactions (1). Phycosphere microbiota inhabited within this distinctive microenvironment have been revealed in a number of phytoplankton assemblages and play crucial roles in aquatic environments (2). The dynamic interplay between host algae and the associated microbiota harbors cross-kingdom exchanges of nutrients, infochemicals, and gene transfer agents (2). However, there is a scarcity of available genome sequences of the phycosphere microbiota of bloom-triggering marine dinoflagellates. During the execution of the Phycosphere Microbiome Project, dozens of cultivable alga-associated bacteria were isolated from a globally distributed toxic dinoflagellate, Alexandrium catenella. Some strains have been identified as new members of the Alphaproteobacteria and Gammaproteobacteria (3–6). For deeply deciphering the mechanisms governing the host-microbe interactome of algal holobionts, draft genomic sequences of the nine bacterial strains are presented.
Bacterial strains of toxic A. catenella LZT09 were isolated according to our previously described protocol (5). For DNA extraction, the strains were cultured in marine 2216 broth at 25 to 28°C with shaking (150 rpm) for 36 to 48 h. DNA extraction and PCR amplification of bacterial 16S rRNA gene sequences of all strains were performed according to the methods described previously (5). The strains were identified taxonomically based on the comparison of 16S rRNA gene sequence similarity using the online EzBioCloud database (http://www.ezbiocloud.net/eztaxon) (7). Genomic DNA was extracted with DNeasy UltraClean DNA kits according to the instructions from Qiagen (Maryland, USA). The Illumina 2 × 250-bp paired-end library was prepared using a TruSeq DNA sample prep kit from Illumina (Massachusetts, USA) according to the manufacturer’s instructions and then sequenced using an Illumina HiSeq 4000 system. Trimmomatic v0.36 with default settings was used for trimming and quality filtering (8). FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used to assess the read quality. The genome assembly for strains of LZ-5T, LZ-14, and LZ-16-2T was performed using SOAPdenovo v2.04 (9), and the other six strains were done with SPAdes v3.5.0 (10). Gene prediction and genomic annotation were performed using NCBI PGAP v1.2.1 (11). Default parameters were used for all software unless otherwise specified. All of the genomes sequenced exceeded 260× coverage, and the characteristics of the nine obtained assemblies are described in Table 1. The availability of genome data for the phycosphere microbiome of toxic A. catenella will offer valuable clues for ongoing comparative studies on alga-bacterium interactions.
TABLE 1.
Summarized genomic features of nine alga-associated heterotrophic proteobacteria isolated from the cultivable phycosphere microbiota of toxic Alexandrium catenella LZT09
| Strain name | Genome length (bp) | G+C (mol%) | No. of genes | No. of reads | Coverage (×) | No. of contigs | N50 (bp) | Assembler | SRA accession no. | GenBank accession no. | No. of tRNAs | No. of rRNAs | No. of ncRNAsa |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Limnobacter sp. LZ-4 | 3,488,419 | 52.5 | 3,298 | 8,534,482 | 422 | 17 | 452,966 | SPAdes v3.5.0 | SRR11279520 | SWKN00000000 | 3 | 39 | 4 |
| Saccharospirillum alexandrii LZ-5T | 4,712,158 | 56.4 | 4,222 | 10,915,266 | 326 | 29 | 1,318,875 | SOAPdenovo v2.04 | SRR11267958 | RCIP00000000 | 3 | 53 | 4 |
| Marinobacter sp. LZ-8 | 4,337,754 | 57.4 | 3,998 | 9,344,736 | 312 | 20 | 882,613 | SPAdes v3.5.0 | SRR11300914 | SWKM00000000 | 4 | 49 | 4 |
| Ponticoccus sp. LZ-14 | 4,615,538 | 63.3 | 4,576 | 12,561,168 | 408 | 111 | 1,271,123 | SOAPdenovo v2.04 | SRR11268417 | RBVZ00000000 | 3 | 40 | 3 |
| Marivita sp. LZ-15-2 | 4,829,700 | 59.2 | 4,745 | 9,197,832 | 263 | 65 | 380,371 | SPAdes v3.5.0 | SRR11267608 | SWKO00000000 | 6 | 42 | 3 |
| Maricaulis sp. LZ-16-1 | 3,348,699 | 63.6 | 3,210 | 10,744,348 | 461 | 12 | 558,629 | SPAdes v3.5.0 | SRR11266721 | SWKP00000000 | 3 | 43 | 4 |
| Haliea alexandrii LZ-16-2T | 3,961,381 | 61.3 | 3,606 | 10,318,956 | 367 | 12 | 905,050 | SOAPdenovo v2.04 | SRR11278742 | RFLW00000000 | 3 | 41 | 4 |
| Maritimibacter sp. LZ-17 | 4,309,600 | 64.3 | 4,269 | 10,762,194 | 375 | 21 | 937,164 | SPAdes v3.5.0 | SRR11266783 | SWKQ00000000 | 3 | 41 | 3 |
| Mameliella sp. LZ-28 | 5,663,795 | 64.9 | 5,548 | 14,028,028 | 372 | 38 | 326,544 | SPAdes v3.5.0 | SRR11285606 | JAANYX000000000 | 8 | 50 | 3 |
ncRNAs, noncoding RNAs.
Data availability.
The genome sequences of the nine bacterial strains were deposited in DDBJ/ENA/GenBank. Detailed information is listed in Table 1.
ACKNOWLEDGMENTS
This work was funded by the NSFC (grant numbers 41876114 and 41206093 to X.-L.Z.), the National Key R&D Program (grant number 2018YFC0311106 to S.-J.W.), the Special Fund of Scientific Innovation Strategy Construction of the High Level Academy of Agriculture Science (grant number R2020YJ-LJ001 to X.Y.), the NSF of Zhejiang Province (grant number LY18D060007 to Q.Y.), the Talent Introduction Fund of ZJOU (grant number 20170228 to Q.Y.), the Special Fund for National Non-profit Institutes (grant numbers 2014M02 and 2012T08 to Q.Y.), and the 948 Project of the MOA (grant number 2015-Z18 to C.-Q.F.).
We also acknowledge the contributions of members of the Phycosphere Microbiome Project (PMP) Consortium (PMPC), Guang Yang at the Key Laboratory of Marine Ecology and Environmental Sciences of CAS, Dong Chen at the Polar Research Institute of China, and Jin-Feng Liu at BGI Shenzhen.
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Associated Data
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Data Availability Statement
The genome sequences of the nine bacterial strains were deposited in DDBJ/ENA/GenBank. Detailed information is listed in Table 1.