Microbial Community Structure and Associations During a Marine Dinoflagellate Bloom

Zhou, Jin; Richlen, Mindy L.; Sehein, Taylor R.; Kulis, David M.; Anderson, Donald M.; Cai, Zhonghua

doi:10.3389/fmicb.2018.01201

Cited by 116 publications

(85 citation statements)

References 125 publications

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“…However, when the HAB enters the postbloom stage, a different picture is apparent, i.e., stochastic processes dominate in this period. This may be due to the disturbance (algal bloom event), which resulted in competition based on limited nutrients or space (45). This is further supported by literature demonstrating that competition contributed to the random process of attached bacterial distribution (46).…”

Section: Discussionsupporting

confidence: 54%

Phycosphere Microbial Succession Patterns and Assembly Mechanisms in a Marine Dinoflagellate Bloom

Zhou

Chen

Ying

et al. 2019

Appl Environ Microbiol

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Given the ecological significance of microorganisms in algal blooming events, it is critical to understand the mechanisms regarding their distribution under different conditions. We tested the hypothesis that microbial community succession is strongly associated with algal bloom stages, and that the assembly mechanisms are cocontrolled by deterministic and stochastic processes. Community structures and underlying ecological processes of microbial populations (attached and free-living bacteria) at three algal bloom stages (pre-, during, and postbloom) over a complete dinoflagellate Scrippsiella trochoidea bloom were investigated. Both attached and free-living taxa had a strong response to the bloom event, and the latter was more sensitive than the former. The contribution of environmental parameters to microbial variability was 40.2%. Interaction analysis showed that complex positive or negative correlation networks exist in phycosphere microbes. These relationships were the potential drivers of mutualist and competitive interactions that impacted bacterial succession. Null model analysis showed that the attached bacterial community primarily exhibited deterministic processes at pre- and during-bloom stages, while dispersal-related processes contributed to a greater extent at the postbloom stage. In the free-living bacterial community, homogeneous selection and dispersal limitation dominated in the initial phase, which gave way to more deterministic processes at the two later stages. Relative contribution analyses further demonstrated that the community turnover of attached bacteria was mainly driven by environmental selection, while stochastic factors had partial effects on the assembly of free-living bacteria. Taken together, these data demonstrated that a robust link exists between bacterioplankton community structure and bloom progression, and phycosphere microbial succession trajectories are cogoverned by both deterministic and random processes. IMPORTANCE Disentangling the mechanisms shaping bacterioplankton communities during a marine ecological event is a core concern for ecologists. Harmful algal bloom (HAB) is a typical ecological disaster, and its formation is significantly influenced by alga-bacterium interactions. Microbial community shifts during the HAB process are relatively well known. However, the assembly processes of microbial communities in an HAB are not fully understood, especially the relative influences of deterministic and stochastic processes. We therefore analyzed the relative contributions of deterministic and stochastic processes during an HAB event. Both free-living and attached bacterial groups had a dramatic response to the HAB, and the relative importance of determinism versus stochasticity varied between the two bacterial groups at various bloom stages. Environmental factors and biotic interactions were the main drivers impacting the microbial shift process. Our results strengthen the understanding of the ecological mechanisms controlling microbial community patterns during the HAB process.

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Section: Discussionsupporting

confidence: 54%

Phycosphere Microbial Succession Patterns and Assembly Mechanisms in a Marine Dinoflagellate Bloom

Zhou

Chen

Ying

et al. 2019

Appl Environ Microbiol

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“…It has been reported that associations with Rhizobiales bacteria might play a crucial role in the fitness of Alexandrium strains, as species of the order Rhizobiales have been frequently reported during the blooms of Alexandrium spp. [43–45]. In addition, bacteria from this order have been found in the benthic assemblage of a coral reef ecosystem [46].…”

Section: Discussionmentioning

confidence: 99%

Isolation and Characterization of aRhizobiumBacterium Associated with the Toxic DinoflagellateGambierdiscus balechii

Yang

Lin

et al. 2019

Preprint

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25Algae-bacteria associations are increasingly being recognized to be important in 26shaping the growth of both algae and bacteria. Bacteria belonging to order 27Rhizobiales are important symbionts of legumes often developing as nodules on plant 28 roots, but have not been widely documented in association with algae. Here, we 29 detected, isolated, and characterized a Rhizobium species from the toxic benthic 30dinoflagellate Gambierdiscus culture. The sequence of 16S rDNA showed 99% 31 identity with that of Rhizobium rosettiformans. To further characterize the bacterium, 32we amplified and sequenced a cell wall hydrolase (CWH)-encoding gene; 33 phylogenetic analysis indicated that this sequence was similar to the homologs of 34Martellela sp. and Hoeflea sp, of order Rhizobiales. We performed PCR using nifH 35 primers to determine whether this bacterium can fix N2; however, the results of 36 sequencing analysis showed that it was closer to chlorophyllide a reductase-encoding 37 gene (bchX), which is similar to nifH. Results of 16S rDNA qPCR showed that 38 compared to that in the early exponential phase, the abundance of this bacterium 39 increased during the late exponential growth phase of Gambierdiscus. When the 40 dinoflagellate culture was subjected to N limitation, the abundance of the bacterium 41 represented by both 16S rDNA and CWH increased. Based on these results and 42 published literature, it is apparent that this Rhizobium bacterium benefits from the 43 association with Gambierdiscus by hydrolyzing and utilizing the extracellular organic 44 matter exudates released by the dinoflagellate. This is the first report of Rhizobium 45 4 species being associated with dinoflagellates, which will shed light on the algae-46 bacteria relationships. 47 7 RESULTS 105 Phylogenies of 16S rDNA and CWH gene sequences from the isolated bacterium 106G. balechii exhibited exponential growth when a sample was collected for 107 bacterium isolation. Random clones were selected when colonies appeared on the 108 marine agar plate. CWH primers were used to screen the bacterial clones that 109 contained the CWH gene. Out of these selected clones, 50 % yielded positive PCR 110 results. 111Sequencing of 16S rDNA amplicons from the CWH-positive colonies revealed 112 Bacterium spp., Bacillus spp., Rhizibium spp., and Flavobacterium spp. to be the 113 closest matches. A Rhizobium species was selected for further characterization. The 114 sequence of the isolated bacterium species (1,362 bp) was 99.93% identical to that of 115 Rhizobium rosettiformans strain W3, which was isolated from groundwater from 116 Lucknow, India [31]. Based on the commonly used species-delineating criterion of 117 16S rDNA identity (97% for prokaryotes), this bacterial strain was classified as 118Rhizobium rosettiformans strain GAMBA-01. The result of phylogenetic analysis 119 verified that this bacterial strain belonged to the same sub-cluster as other Rhizobium 120 strains (Fig. 1). 121 122Conserved domain searches in BLASTp revealed that the CWH sequence c...

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“…This was reflected in the Simpson index as well as the indices for September 2017 being lower than those of the August 2016 or March 2017 samples. Similarly, Zhou et al (2018) demonstrated that the Simpson Indices for bacteria increased after the onset of an algal bloom (Brackish peat, September 2017) whereas the Shannon indices was at the lowest (Brackish peat, March 2017) (when assuming that the region in which phytoplankton blooms occur is the brackish peat region). Overall, there was greater diversity (based on Shannon Indices) in the dry season (August 2016) than the wet seasons (March and September 2017) whereas there were greater OTUs in the wet season (Observed index).…”

Section: Diversity and Shifts In Bacterial Communities Along The Rajamentioning

confidence: 91%

Biogeographical distribution of Microbial Communities along the Rajang River-South China Sea Continuum

Sia¹,

Zhu²,

Zhang³

et al. 2019

Preprint

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Abstract. Microbial community composition and diversity in freshwater habitats, especially in lotic environments, are much less studied compared to marine and soil communities. The Rajang River is the main drainage system for central Sarawak in Malaysian Borneo and passes through peat domes whereby peat-rich material is being fed into the system and eventually into the southern South China Sea. Microbial communities found within peat-rich systems are important biogeochemical cyclers in terms of methane and carbon dioxide sequestration. To address the critical lack of knowledge about microbial communities in tropical (peat-draining) rivers, this study represents the first seasonal assessment targeted at establishing a foundational understanding of the microbial communities of the Rajang River-South China Sea continuum. This was carried out utilizing 16S rRNA gene amplicon sequencing via Illumina MiSeq in size-fractionated samples (0.2 and 3.0 μm GF/C filter membranes) covering different biogeographical features/sources from headwaters to coastal waters. The microbial communities found along the Rajang river exhibited taxa common to rivers (i.e. the predominance of β-Proteobacteria) while estuarine and marine regions exhibited taxa that were common to the aforementioned regions as well (i.e. predominance of α- and γ-Proteobacteria). This is in agreement with studies from other rivers which observed similar changes along the salinity gradients. In terms of particulate versus free-living bacteria, nonmetric multi-dimensional scaling (NMDS) results showed similarly distributed microbial communities with varying separation between seasons. Distinct patterns were observed based on linear models as a result of the changes in salinity along with variation of other biogeochemical parameters. Alpha diversity indices indicated that microbial communities were higher in diversity upstream compared to the marine and estuarine regions whereas anthropogenic perturbations led to increased richness but less diversity. Despite the observed changes in bacterial community composition and diversity that occur along the Rajang River to sea continuum, the PICRUST predictions showed minor variations. The results provide essential context for future studies such as further analyses on the ecosystem health in response to anthropogenic land-use practices and probable development of biomarkers to improve the monitoring of water quality in this region.

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Microbial Community Structure and Associations During a Marine Dinoflagellate Bloom

Cited by 116 publications

References 125 publications

Phycosphere Microbial Succession Patterns and Assembly Mechanisms in a Marine Dinoflagellate Bloom

Phycosphere Microbial Succession Patterns and Assembly Mechanisms in a Marine Dinoflagellate Bloom

Isolation and Characterization of aRhizobiumBacterium Associated with the Toxic DinoflagellateGambierdiscus balechii

Biogeographical distribution of Microbial Communities along the Rajang River-South China Sea Continuum

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