Edited by: Olga Lage, University of Porto, Portugal
Reviewed by: Xiaoqian Yu, University of Vienna, Austria; Catarina Magalhães, University of Porto, Portugal
This article was submitted to Aquatic Microbiology, a section of the journal Frontiers in Microbiology
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The marine phytoplankton community is a main contributor to primary production and plays important roles in regulating energy export, carrying out more than half of the photosynthetic carbon fixation in euphotic zones (
From the viewpoint of ecological processes, microbial communities are driven by a combination of stochastic and deterministic processes (
For decades, blooms of
The surface seawater samples used in this study were collected from a water depth of 0.5 m using a rosette of Niskin bottles attached to a CTD probe frame during the Open Cruises of Qinzhou Bay (
One-liter seawater samples were collected in parallel, filtered through filters (47 mm, Whatman GF/F nominal pore size, Maidstone, United Kingdom), and frozen at −20°C until analysis. The concentrations of total dissolved nitrogen (TDN), NO3–, and NH4+ were determined using the Cu–Cd column reduction and indophenol blue color formation methods, respectively (
To study
Total DNA of the 24 samples was extracted (Mo-Bio PowerWater DNA Isolation Kit, Carlsbad, CA, United States) from the 0.22-μm filters. DNA yield and purity were measured by a NanoDrop spectrophotometer (Delaware, United States). For sequencing, the V3 and V4 regions of the 16S ribosomal RNA gene from the seawater were amplified with the bacterial primers 341F (CCTACGGGNGGCWGCAG) and 805R (GACTACHVGGGTATCTAATCC) with sample-specific barcodes (
Sequencing data were analyzed using the single software platform MOTHUR v.1.35.1 (
Phylogenetic maximum likelihood-approximation trees were constructed in FastTree software (
For a single community, an NRI and NTI greater than +2 indicate that coexisting taxa are more closely related than expected by chance (phylogenetic clustering), indicating a dominant role of deterministic environmental filtering (
Data normality was tested using the Shapiro–Wilk test. After filtering of the raw OTU table, the diversity within each bacterial community (α-diversity) was assessed by diversity indices, including the Shannon index, the Chao index (SChao), the Simpson index (1/D), and Good’s coverage. Additionally, ANOVA, PERMANOVA, and Spearman’s correlation were performed using the RAM and vegan packages in the R language. Random forest analysis was applied to obtain the important indicator taxa using the random forest package with 1000 trees and default settings (
After removing chimeras, a total of 135,841 OTUs were obtained from 72 samples, with 586–3796 (mean: 1887 ± 649) OTUs in each sample (
The relative abundances of bacterial communities at the phylum level during the
The α-diversity indices in different groups. The differences between pairs of two groups were tested by the Wilcoxon test. ns, not significant. ∗
The collected
Phylogenetic relatedness based on NRI and NTI of marine water samples.
Blooms period | Mean NRI ± SD | Null model percentile | Mean NTI ± SD | Null model percentile |
BB | 2.02 ± 1.16b | 0.145 | 2.64 ± 0.58c | 0.006 |
DB | 2.33 ± 0.38a | 0.016 | 2.53 ± 0.58c | 0.002 |
AB | 1.45 ± 0.37b | 0.927 | 0.43 ± 0.28d | 0.459 |
Cell number of P. globasa | −0.22 | 0.24 | 0.18 | 0.46 |
During sample collection, temperature, salinity, pH, and dissolved oxygen (DO) were also measured. The temperature range was 12.38–16.98°C. The salinity range was 22.71–29.36 ppt (
Regressions between environmental changes and microbial community similarity. The X-axis indicates the ln-transformed environmental distance (Euclidean), and the Y-axis indicates the ln-transformed Bray–Curtis distance. The solid blue line indicates the linear spline fit. The gray shadow represents the 95% confidence interval.
Distance-based redundancy analysis (db RDA) ordination plots of the bacterial community–environment relationships. BB, before
We also investigated the most important genera in different groups using the random forest method. The results showed that
Top 40 most important genera for random forest classification. Left, the top 40 taxa were assessed by the Gini index, which indicated the importance of each genus in distinguishing various groups; middle, read abundances of the top 40 genera; right, the Spearman’s correlations between the relative abundances of the top 40 genera and the environmental parameters. PG density,
VPA was performed to quantify the relative contributions of different environmental parameters to changes in bacterial community structure.
Variation partitioning analysis of
Path model based on the effects of environmental variables and relative abundance, diversity, and phylogenetic relatedness of the microbial community in marine waters with various
Marine surface microbes are directly linked to ecosystem processes such as decomposition and biogeochemical cycles. The consequences of altered nutrient concentrations or altered phytoplankton communities may be reflected in changes in the ability to decompose or in the rate of degradation of organic materials. Therefore, it is important to explore the ecological processes of natural free-living microbial communities during environmental phytoplankton blooms. The prymnesiophyte
Recent phylogenetic analyses of the marine microbiome have been carried out on both experimental and natural phytoplankton blooms, and the bacterial lineages of the most abundant bloom-associated microbes are now well-demonstrated (
NMDS analysis indicated that the β-diversity based on Bray–Curtis dissimilarity of free-living bacterial communities in marine waters in the AB group was distinct from that in the BB and DB groups (
Moreover, PLS path modeling and multiple regression of
Although there is an extensive literature examining microbial community composition and gene expression patterns during phytoplankton blooms in marine environments (
Our results confirmed the simultaneous effects of stochastic and deterministic drivers on bacterial community assembly during
The most striking feature of
This study revealed the interactive effects of both
The datasets generated for this study were deposited in NCBI Sequence Read Archive (SRA) under BioProject number
NL and ZK prepared the manuscript. HZ, GJ, and QX analyzed the data. JT, XL, JW, HL, and CT prepared the sampling and treating the samples. All authors contributed to the article and approved the submitted version.
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
We appreciated Prof. Jonathan M. Adams at the Nanjing University for editing the language.
The Supplementary Material for this article can be found online at: