Role of environmental factors for the vertical distribution (0–1000 m) of marine bacterial communities in the NW Mediterranean Sea

Abstract. Bacterioplankton plays a central role in energy and matter fluxes in the sea, yet the factors that constrain its variation in marine systems are still poorly understood. Here we use the explanatory power of direct multivariate gradient analysis to evaluate the driving forces exerted by environmental parameters on bacterial community distribution in the water column. We gathered and analysed data from a one month sampling period from the surface to 1000 m depth at the JGOFS-DYFAMED station (NW Mediterranean Sea). This station is characterized by very poor horizontal advection currents which makes it an ideal model to test hypotheses on the causes of vertical stratification of bacterial communities. Capillary electrophoresis single strand conformation polymorphism (CE-SSCP) fingerprinting profiles analyzed using multivariate statistical methods demonstrated a vertical zonation of bacterial assemblages in three layers, above, in or just below the chlorophyll maximum and deeper, that remained stable during the entire sampling period. Through the use of direct gradient multivariate ordination analyses we demonstrate that a complex array of biogeochemical parameters is the driving force behind bacterial community structure shifts in the water column. Physico-chemical parameters such as phosphate, nitrate, salinity and to a lesser extent temperature, oxygen, dissolved organic carbon and photosynthetically active radiation acted in synergy to explain bacterial assemblages changes with depth. Analysis of lipid biomarkers of organic matter sources and fates suggested that bacterial community structure in the surface layers was in part explained by lipids of chloroplast origin. Further detailed analysis of pigment-based phytoplankton diversity gave evidence of a compartmentalized influence of several phytoplankton groups on bacterial community structure in the first 150 m depth.

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Role of environmental factors for the vertical distribution (0–1000 m) of marine bacterial communities in the NW Mediterranean Sea

Biogeosciences Discussions ◽

10.5194/bgd-5-2131-2008 ◽

2008 ◽

Vol 5 (3) ◽

pp. 2131-2164 ◽

Cited By ~ 9

Author(s):

J. F. Ghiglione ◽

C. Palacios ◽

J. C. Marty ◽

G. Mével ◽

C. Labrune ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Sampling Period ◽

Multivariate Statistical ◽

Marine Systems ◽

Nw Mediterranean ◽

Nw Mediterranean Sea ◽

Bacterial Assemblages

Abstract. Bacterioplankton play a central role in energy and matter fluxes at the sea, yet the factors that constrain their variation in the marine systems are still poorly understood. Here we show the explanatory power of multivariate statistical analysis of bacterial community structures coupled with fine measurements of numerous environmental parameters. We gathered and analysed data from a one month sampling period from the surface to 1000 m depth at the JGOFS-DYFAMED station (NW Mediterranean Sea). This station is characterized by very poor horizontal advection currents what makes it an ideal model to test hypothesis on the causes of vertical stratification of bacterial communities. Capillary electrophoresis single strand conformation polymorphism (CE-SSCP) fingerprinting profiles analyzed using multivariate statistical methods demonstrated a vertical zonation of bacterial assemblages in three layers, above, in or just below the chlorophyll maximum and deeper, that remained stable during the entire sampling period. Through the use of direct gradient multivariate ordination analyses we demonstrate that a complex array of biogeochemical parameters is the driving force behinds bacterial community structure shifts in the water column. Physico-chemical parameters such as phosphate, nitrate, salinity and to a lesser extend temperature, oxygen, dissolve organic carbon and photosynthetically active radiation acted in synergy to explain bacterial assemblages changes with depth. Analysis of lipid biomarkers of the organic matter sources and fates suggested that bacterial community structure at the surface layers was in part explained by lipids from chloroplast origin. Further detailed analysis of pigment-based phytoplankton diversity gave evidence of a compartmentalized influence of several phytoplankton groups on bacterial community structure in the first 150 m depth. This study is probably the first example of an analysis employing a complex environmental dataset in combination with microbial community profiles to unravel the mechanisms underneath bacterial assemblages in marine systems.

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Short scale variations in nutrients, ectoenzymatic activities and bottom-up effects on bacterial production and community structure during late summer-autumn transition in the open NW Mediterranean Sea

Biogeosciences Discussions ◽

10.5194/bgd-6-687-2009 ◽

2009 ◽

Vol 6 (1) ◽

pp. 687-727 ◽

Cited By ~ 5

Author(s):

F. Van Wambeke ◽

J-F. Ghiglione ◽

J. Nedoma ◽

G. Mével ◽

P. Raimbault

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Mediterranean Sea ◽

Mixed Layer ◽

Bacterial Production ◽

Bacterial Community Structure ◽

Late Summer ◽

Bottom Up ◽

Nw Mediterranean ◽

Nw Mediterranean Sea

Abstract. We examined the vertical and temporal dynamics of nutrients, ectoenzymatic activities under late summer-fall transition period (September–October 2004) in NW Mediterranean Sea in relation to temporal change in factors limiting bacterial production. The depth of the mixed layer (12.8±5.3 m) was extremely stable until the onset of the destratification period after 11 October, creating a zone where diffusion of nutrient from the much deeper phosphacline (69±12 m) and nitracline (50±8 m) was probably strongly limited. However during the second half of the cruise, a shallowing of nutriclines occured, particularly marked for nitracline. Hence, the nitrate to phosphate ratio within the mixed layer, although submitted to a high short term variability, shifted the last week of the cruise from 1.1±1.2 to 4.6±3.8, and nitrate increased by a factor 2 (0.092±0.049 μM). A corresponding switch from more than one limitation (PN) to P-only limitation of bacterial production was observed during the month as detected by enrichment bioassays. Differences in the identity of the limiting nutrient in surface (5 m: N and P at the beginning, strictly P at the end of the study) versus 80 m (labile carbon) influence greatly bacterial community structure shift between these two layers. The two communities (5 and 80 m) reacted rapidly (24 h) to changes in nutrient concentrations by drastic modification of total and active population assemblages resulting in changes in activity. For bacterial production values less than 10 ng C l−1h−1 (associated to deeper layers), aminopeptidase and lipase exhibited higher activity relative to production whereas phosphatase varied in the same proportions than BP on the range of activities tested. Our results illustrate the effect of bottom-up control on bacterial community structure and activities in the epipelagic NW Mediterranean Sea.

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Bottom up effects on bacterioplankton growth and composition during summer-autumn transition in the open NW Mediterranean Sea

Biogeosciences ◽

10.5194/bg-6-705-2009 ◽

2009 ◽

Vol 6 (4) ◽

pp. 705-720 ◽

Cited By ~ 34

Author(s):

F. Van Wambeke ◽

J.-F. Ghiglione ◽

J. Nedoma ◽

G. Mével ◽

P. Raimbault

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Mediterranean Sea ◽

Mixed Layer ◽

Bacterial Production ◽

Bacterial Community Structure ◽

Bottom Up ◽

Production Values ◽

Nw Mediterranean ◽

Nw Mediterranean Sea

Abstract. We examined the vertical and temporal dynamics of nutrients, ectoenzymatic activities under late summer-fall transition period (September–October 2004) in NW Mediterranean Sea in relation to temporal change in factors limiting bacterial production. The depth of the mixed layer (12.8±5.3 m) was extremely stable until the onset of the destratification period after 11 October, creating a zone where diffusion of nutrient from the much deeper phosphacline (69±12 m) and nitracline (50±8 m) was probably strongly limited. However after 1st October, a shallowing of nutriclines occured, particularly marked for nitracline. Hence, the nitrate to phosphate ratio within the mixed layer, although submitted to a high short term variability, shifted the last week of the cruise from 1.1±1.2 to 4.6±3.8, and nitrate increased by a factor 2 (0.092±0.049 μM). A corresponding switch from more than one limitation (PN) to P-only limitation of bacterial production was observed during the month as detected by enrichment bioassays. Differences in the identity of the limiting nutrient in surface (5 m: N and P at the beginning, strictly P at the end of the study) versus 80 m (labile carbon) influence greatly bacterial community structure shift between these two layers. The two communities (5 and 80 m) reacted rapidly (24 h) to changes in nutrient concentrations by drastic modification of total and active population assemblages resulting in changes in activity. For bacterial production values less than 10 ng C l−1 h−1 (associated to deeper layers), aminopeptidase and lipase exhibited higher activity relative to production whereas phosphatase varied in the same proportions than BP on the range of activities tested. Our results illustrate the effect of bottom-up control on bacterial community structure and activities in the epipelagic NW Mediterranean Sea.

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Vertical Distribution of Bacterial Community in Water Columns of Reservoirs With Different Trophic Conditions During Thermal Stratification

Frontiers in Environmental Science ◽

10.3389/fenvs.2021.632089 ◽

2021 ◽

Vol 9 ◽

Author(s):

Yihong Yue ◽

Ling Cai ◽

Yi Tang ◽

Yuanyuan Zhang ◽

Ming Yang ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Water Column ◽

Water Depth ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Thermal Stratification ◽

Absolute Abundance ◽

Gene Copies ◽

Water Columns

Water eutrophication is a global ecological issue, and thermal stratification of water bodies can enable eutrophication. We examined bacterial communities in the stratified water columns and sediments in two different trophic reservoirs along the Wujiang River using quantitative real-time PCR and high-throughput sequencing. Bacterial 16S rRNA gene copies varied from 3.70 × 107 to 5.27 × 108 copies/L in the water column of Hongjiadu (HJD) Reservoir (60 m water depth) with slightly stratified variation; while in Wujiangdu (WJD) Reservoir (70 m water depth), bacterial abundance decreased markedly from the surface to the bottom(1.74 × 109 to 2.38 × 107 copies/L). The vertical distribution patterns of bacteria in both reservoirs resembled those of water Chlorophyll a (Chla) concentrations. The abundance was negatively correlated with water depth (D), total nitrogen (TN), nitrate (NO3–-N), and positively correlated with water temperature (T) and dissolved oxygen (DO) level. In contrast, the alpha diversity of bacteria showed the opposite trend in the vertical water column. Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant phyla in the water column of both reservoirs. Compared to WJD Reservoir, HJD Reservoir displayed marked vertical spatial difference in bacterial community structure during thermal stratification. In particular, Pseudomonas was frequently detected at the bottom of the HJD Reservoir. These results were consistent with predictive metagenomic profiling that revealed different vertical functional variation patterns of the bacterial communities in the two reservoirs. The bacterial community structure of HJD Reservoir was associated with water D, ammonium (NH4+-N), nitrite (NO2–-N), and total phosphorus (TP). The community structure of WJD Reservoir was related to water T, Chla, NO3–-N, and TN. The findings highlighted the important roles played by thermal stratification and nutrients in shaping the water bacterial community structure. Additionally, the absolute abundance of water nitrifiers (AOB gene copies) and denitrifiers (narG, nirS, norB, and nosZ gene copies) displayed significant vertical differences in the water columns of both reservoirs. Gene copies involved in denitrification were significantly higher than those involved in nitrification. Water phosphorus and nitrogen contents were important variables influencing the absolute abundance of ammonia oxidizers and denitrifying bacteria, respectively. Our study revealed that the emergence of thermal stratification was responsible for the vertical stratification of bacteria in water and affected the bacterial community structure together with nutrients.

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Effects of Plastic Debris on the Biofilm Bacterial Communities in Lake Water

Water ◽

10.3390/w13111465 ◽

2021 ◽

Vol 13 (11) ◽

pp. 1465

Author(s):

Chao Shen ◽

Liuyan Huang ◽

Guangwu Xie ◽

Yulai Wang ◽

Zongkai Ma ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Diversity Index ◽

Plastic Substrate ◽

Simpson Index ◽

Plastic Debris ◽

Plastic Substrates ◽

Wiener Diversity Index

Increasing discharge of plastic debris into aquatic ecosystems and the worsening ecological risks have received growing attention. Once released, plastic debris could serve as a new substrate for microbes in waters. The complex relationship between plastics and biofilms has aroused great interest. To confirm the hypothesis that the presence of plastic in water affects the composition of biofilm in natural state, in situ biofilm culture experiments were conducted in a lake for 40 days. The diversity of biofilm attached on natural (cobble stones (CS) and wood) and plastic substrates (Polyethylene terephthalate (PET) and Polymethyl methacrylate (PMMA)) were compared, and the community structure and composition were also analyzed. Results from high-throughput sequencing of 16S rRNA showed that the diversity and species richness of biofilm bacterial communities on natural substrate (observed species of 1353~1945, Simpson index of 0.977~0.989 and Shannon–Wiener diversity index of 7.42~8.60) were much higher than those on plastic substrates (observed species of 900~1146, Simpson index of 0.914~0.975 and Shannon–Wiener diversity index of 5.47~6.99). The NMDS analyses were used to confirm the taxonomic significance between different samples, and Anosim (p = 0.001, R = 0.892) and Adonis (p = 0.001, R = 808, F = 11.19) demonstrated that this classification was statistically rigorous. Different dominant bacterial communities were found on plastic and natural substrates. Alphaproteobacterial, Betaproteobacteria and Synechococcophycideae dominated on the plastic substrate, while Gammaproteobacteria, Phycisphaerae and Planctomycetia played the main role on the natural substrates. The bacterial community structure of the two substrates also showed significant difference which is consistent with previous studies using other polymer types. Our results shed light on the fact that plastic debris can serve as a new habitat for biofilm colonization, unlike natural substrates, pathogens and plastic-degrading microorganisms selectively attached to plastic substrates, which affected the bacterial community structure and composition in aquatic environment. This study provided a new insight into understanding the potential impacts of plastics serving as a new habitat for microbial communities in freshwater environments. Future research should focus on the potential impacts of plastic-attached biofilms in various aquatic environments and the whole life cycle of plastics (i.e., from plastic fragments to microplastics) and also microbial flock characteristics using microbial plastics in the natural environment should also be addressed.

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Significant Differences in the Gut Bacterial Communities of Hooded Crane (Grus monacha) in Different Seasons at a Stopover Site on the Flyway

Animals ◽

10.3390/ani10040701 ◽

2020 ◽

Vol 10 (4) ◽

pp. 701 ◽

Cited By ~ 1

Author(s):

Fengling Zhang ◽

Xingjia Xiang ◽

Yuanqiu Dong ◽

Shaofei Yan ◽

Yunwei Song ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Bacterial Community Composition ◽

Stopover Site ◽

Intestinal Bacterial Community ◽

Hooded Crane ◽

Grus Monacha

Intestinal bacterial communities form an integral component of the organism. Many factors influence gut bacterial community composition and diversity, including diet, environment and seasonality. During seasonal migration, birds use many habitats and food resources, which may influence their intestinal bacterial community structure. Hooded crane (Grus monacha) is a migrant waterbird that traverses long distances and occupies varied habitats. In this study, we investigated the diversity and differences in intestinal bacterial communities of hooded cranes over the migratory seasons. Fecal samples from hooded cranes were collected at a stopover site in two seasons (spring and fall) in Lindian, China, and at a wintering ground in Shengjin Lake, China. We analyzed bacterial communities from the fecal samples using high throughput sequencing (Illumina Mi-seq). Firmicutes, Proteobacteria, Tenericutes, Cyanobacteria, and Actinobacteria were the dominant phyla across all samples. The intestinal bacterial alpha-diversity of hooded cranes in winter was significantly higher than in fall and spring. The bacterial community composition significantly differed across the three seasons (ANOSIM, P = 0.001), suggesting that seasonal fluctuations may regulate the gut bacterial community composition of migratory birds. This study provides baseline information on the seasonal dynamics of intestinal bacterial community structure in migratory hooded cranes.

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Diel and Seasonal Variations in Abundance, Activity, and Community Structure of Particle-Attached and Free-Living Bacteria in NW Mediterranean Sea

Microbial Ecology ◽

10.1007/s00248-006-9189-7 ◽

2007 ◽

Vol 54 (2) ◽

pp. 217-231 ◽

Cited By ~ 106

Author(s):

J. F. Ghiglione ◽

G. Mevel ◽

M. Pujo-Pay ◽

L. Mousseau ◽

P. Lebaron ◽

...

Keyword(s):

Community Structure ◽

Mediterranean Sea ◽

Seasonal Variations ◽

Free Living ◽

Nw Mediterranean ◽

Nw Mediterranean Sea ◽

Living Bacteria

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Comparative analysis of the composition of bacterial communities from two constructed wetlands for municipal and swine wastewater treatment

Journal of Water and Health ◽

10.2166/wh.2009.123 ◽

2009 ◽

Vol 8 (1) ◽

pp. 147-157 ◽

Cited By ~ 9

Author(s):

Paula Arroyo ◽

Gemma Ansola ◽

Ivan Blanco ◽

Patricia Molleda ◽

Estanislao de Luis Calabuig ◽

...

Keyword(s):

Wastewater Treatment ◽

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Typha Latifolia ◽

Treatment System ◽

Swine Wastewater ◽

Wastewater Treatment System ◽

Wastewater Treatment Systems

This work provides information about bacterial community structure in natural wastewater treatment systems treating different types of wastewater. The diversity and composition of bacterial communities associated with the rhizosphere of Typha latifolia and Salix atrocinerea were studied and compared among two different natural wastewater treatment systems, using the direct sequencing of the 16S ribosomal RNA codifying genes. Phylogenetic affiliations of the bacteria detected allowed us to define the main groups present in these particular ecosystems. Moreover, bacterial community structure was studied through two diversity indices. Ten identified and five non-identified phyla were found in the samples; the phylum Proteobacteria was the predominant group in the four ecosystems. The results showed a bacterial community dominated by beta-proteobacteria and a lower diversity value in the swine wastewater treatment system. The municipal wastewater treatment system presented a high diverse community in both macrophytes (Typha latifolia and Salix atrocinerea), with gamma-proteobacteria and alpha-proteobacteria, respectively, as the most abundant groups.

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Effects of Long-Term Elevated CO2 on Rhizosphere and Bulk Soil Bacterial Community Structure in Pinus sylvestriformis Seedlings Fields

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.343-344.351 ◽

2011 ◽

Vol 343-344 ◽

pp. 351-356

Author(s):

Xia Jia ◽

Chun Juan Zhou

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Denaturing Gradient Gel Electrophoresis ◽

Pinus Sylvestriformis ◽

Soil Bacterial Community Structure ◽

Gradient Gel Electrophoresis ◽

Polymerase Chain

The effect of long-term elevated CO2(as open top chambers) on rhizosphere and bulk bacterial community structure in Pinus sylvestriformis seedlings field was investigated in July, August, and September. The bacterial communities were processed by Denaturing Gradient Gel Electrophoresis (DGGE) analysis of bacterial 16S rDNA fragments amplified by PCR (Polymerase Chain Reaction) from DNA extracted directly from soil. DGGE profiles from rhizosphere samples showed large changes in rhizosphere bacterial community under elevated CO2compared to ambient except for that in September. For bulk samples, bacterial community structure changed when exposed to elevated CO2in three months. With the exception of bulk samples in August, a similitude of bacterial communities structures existed between different elevated CO2concentrations by analyzing UPGMA dendrogram based on Jaccard’s coefficient.

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