Diversity and composition of bacterial community in the rhizosphere sediments of submerged macrophytes revealed by 454 pyrosequencing

Microbial community diversity of an integrated constructed wetland used for treatment of sewage

The microbial community diversity in Constructed Wetland System (CWS) plays a key role in the removal of pollutants from waste water. An integrated functional CWS developed at Neela Hauz Biodiversity Park, Delhi was selected to assess the diversity in composition and structure of microbial community diversity of sludge and sediment of CWS, based on metagenomic approach using 16S rRNA genes. The sediment showed higher diversity than sludge and both formed distinct clusters. The taxonomic structure of the microbial community of CWS is represented by 6,731 OTUs distributed among 2 kingdoms, 103 phyla, 227 classes, 337 orders, 320 families, 295 identified genera, and 84 identified species. The relative abundance of top 5 dominant phyla of sludge and sediment varied from 3.77% (Acidobacteria) to 35.33% (Proteobacteria) and 4.07% (Firmicutes) to 28.20% (Proteobacteria), respectively. The range of variation in relative abundance of top 5 dominant genera of sludge and sediment was 2.58% (Hyphomicrobium) to 6.61% (Planctomyces) and 2.47% (Clostridium) to 4.22% (Syntrophobacter), respectively. The rich microbial diversity of CWS makes it perform better in pollutants removal (59.91-95.76%) than other CWs. Based on the abundance values of taxa, the taxa are grouped under four frequency distribution classes-abundant (>20), common (10-19), rare (5-9), and very rare (1-4). The unique structure of microbial communities of integrated CWS is that the number of abundant taxa decreases in descending order of taxonomic hierarchy, while the number of rare and very rare taxa increases. For example, the number of abundant phyla was 14 and 21 in sludge and sediment, respectively and both communities have only 3 abundant genera each. This is in contrast to 4 and 17 very rare phyla in sludge and sediment, respectively and both the communities have 114 and 91 very rare genera, respectively. The outcomes of the study is that the integrated CWS has much higher microbial community diversity than the diversity reported for other CWs, and the rich diversity can be used for optimizing the performance efficiency of CWS in the removal of pollutants from waste water. Such structural diversity might be an adaptation to heterogeneous environment of CWS.

Spatio-temporal dynamic diversity of bacterial alkaline phosphatase phoD gene and its environmental drivers in sediments during algal blooms: A case study of shallow Lake Taihu

Bacterial alkaline phosphatase encoded by the phoD gene is essential for phosphorus (P) cycling in ecosystems. Until now, knowledge of the phoD gene diversity in shallow lake sediments is still lacking. In this study, from early to late stage of cyanobacterial blooms, we investigated the dynamic changes of the abundance of phoD gene (hereafter phoD abundance) and phoD-harboring bacterial community composition (hereafter phoD-harboring BCC) in sediments from different ecological regions of Lake Taihu, the third-largest shallow freshwater lake in China, as well as explored their environmental driving factors. Results showed that phoD abundance in the sediments of Lake Taihu showed spatiotemporal heterogeneity. The highest abundance was found in macrophyte-dominated area (mean 3.25*10⁶copies/g DW), where Haliangium and Aeromicrobium were identified as the major contributors. Due to the negative impact of Microcystis species, phoD abundance decreased significantly (by 40.28% on average) during cyanobacterial blooms in all other regions except the estuary area. The phoD abundance in sediment was positively correlated with total organic carbon (TOC) and total nitrogen (TN). However, the relationship between phoD abundance and alkaline phosphatase activity (APA) varied with time, showing positive correlation (R² = 0.763, P < 0.01) in the early stage of cyanobacterial blooms, but not (R² = -0.052, P = 0.838) in the later stage. The predominant phoD-harboring genera in sediments were Kribbella, Streptomyces and Lentzea, all of which belong to Actinobacteria. Non-metric multidimensional scaling (NMDS) analysis revealed that the spatial heterogeneity of phoD-harboring BCC in the sediments of Lake Taihu was significantly higher than the temporal heterogeneity. TP and sand were the principle environmental factors affecting the phoD-harboring BCC in the sediments of the estuary area, while DO, pH, organic phosphorus (Po) and diester phosphorus were the key driving factors for other lake regions. We concluded that the C, N, and P cycles in sediments might work in concert. This study extends the understanding of the phoD gene diversity in shallow lake sediments.

Toward understanding submersed macrophyte Vallisneria natans-microbe partnerships to improve remediation potential for PAH-contaminated sediment

Rhizodegradation using submersed macrophytes Vallisneria natans (V. natans) is a promising biotechnology with the potential to restore polycyclic aromatic hydrocarbon (PAH)-contaminated sediments. However, how different sediment types influence the rhizoremediation outcome and the characterization of microbial community along the sediment-V. natans continuum is poorly understood. Here, we collect V. natans, sediments and overlying water from two types of vegetation zones with different levels of PAHs pollutions and set up sediment microcosms for phytoremediation tests. V. natans presence was particularly useful for PAHs remediation in the highly contaminated sites and had a significant effect on PAHs rhizodegradation and microbial communities, especially rhizosphere sediments. The structural composition of microbial communities along the sediment-plant continuum was shaped predominantly by compartment niche of V. natans. Moreover, selective enrichment of specific microbial taxa like Herbaspirillum (relative abundance = 94.80%) in endosphere of V. natans was observed. Herbaspirillum could use PAH as carbon source and promote the growth of plants. In the highly contaminated sediment, V. natans could recruit these bacteria for toxicant degradation into the root interior. Thus, understanding the complex V. natans-microbe interactions could help set up novel decontamination strategies based on the rhizosphere and root interior interactions between plants and their microbial associates.

Mitigation of Eutrophication in a Shallow Lake: The Influences of Submerged Macrophytes on Phosphorus and Bacterial Community Structure in Sediments

Remediating water eutrophication is critical for maintaining healthy and sustainable development of lakes. The aim of this study was to explore the seasonal variation in phosphorus (P) speciation and bacterial community structure in sediments of Qin Lake (Taizhou, Jiangsu Province, China) associated with the growth of submerged macrophyte Vallisneria natans. The differences in sediment bacterial diversity and community structure between V. natans growing and control areas were analyzed over a period of one year. The results showed that V. natans growth reduced the total P and organic matter contents of the sediments and increased the bioavailable iron (Fe) and Fe-bound P contents. The α-diversity of sediment bacteria was significantly higher in the presence of V. natans than in the controls during the vigorous plant growth stage. In the presence of V. natans, there was a higher relative abundance of Proteobacteria and lower relative abundances of Chloroflexi and Acidobacteria. The Fe(II) content in the sediment had a larger influence on the spatial distribution of bacterial communities than sediment Fe-bound P, organic matter, and Fe(II) contents. V. natans growth could reshape sediment bacterial community structure in the shallow lake, which, in turn, enhanced P immobilization in the sediments and thereby improved the water quality.

Effects of root exudates on rhizosphere bacteria and nutrient removal in pond-ditch circulation systems (PDCSs) for rural wastewater treatment

Pond-ditch circulation system (PDCS) is a promising remediation strategy for rural wastewater treatment. Aquatic plants play nonnegligible roles in the nutrient removal of the PDCS. However, mechanisms of root exudates regulating nutrient removal in PDCSs remained unclear. In our study, the PDCS achieved higher total nitrogen (TN) and phosphorus (TP) removal rates (72.7-97.4%) compared to the static system. Protein contents in root exudates of the PDCS ranged from 0.041 to 1.332 mg L^-1, showing negative associations with Simpson index. Lactic acid and tartaric acid in the PDCS varied from 0.045 to 0.380 mg L^-1 and 0.024 to 5.446 mg L^-1, which were tightly linked with TN, TP, and TP removal rates and most sediment properties, especially sediment total nitrogen (STN) and total organic carbon (TOC), and sediment inorganic phosphorus (SIP). Moreover, the top 3 relative dominant genus were Bacillus (0.11%-17.90%), Geobacter (0.35%-12.04%), and Clostridium sensu stricto 1 (0.14%-12.05%), which might be the predominant groups in nutrient removal of PDCSs. RDA results indicated that lactic acid, protein, and amino acids were positively correlated with Geobacter; while Bacillus was significantly affected by water content. Path analysis further demonstrated that the indirect effect of secretion from plant roots on nutrient removal rates was mainly through modulating bacteria diversity and relative abundance. Taken together, root exudates, especially protein, amino acids, and lactic acid, altered rhizosphere microbial relative abundance and diversity, where the impacts were bacterial species-dependent.

Bacterial succession in epiphytic biofilms and deciduous layer sediments during Hydrilla verticillata decay: A field investigation

Submersed macrophytes decay is an important natural process and has important role in mass and energy flow in aquatic ecosystems. However, little is known about the dynamical changes in nutrients release and bacterial community during submersed macrophyte decay in natural environment. In this study, a field observation was conducted in a wetland dominated with Hydrilla verticillata for 36 days. Increase of H₂O₂ and malondialdehyde (MDA) content and decrease of soluble proteins concentration were detected in leaves during H. verticillata decay. Meanwhile, ammonium-N, soluble microbial products (SMP) and TOC concentration increased in overlying water. According to bacterial 16S rRNA Illumina sequencing analysis, the Shannon values were lower in epiphytic biofilms than deciduous layer sediments. The relative abundances of Proteobacteria, Cyanobacteria and Actinobacteria were higher in epiphytic biofilms than in deciduous layer sediments (P < 0.05). Co-occurrence network analyses showed that a total of 578 and 845 pairs of correlations (|r| > 0.6) were identified from 122 and 112 genera in epiphytic biofilms and deciduous layer sediments, respectively. According to co-occurrence patterns, eight hubs were mainly from phyla Proteobacteria, Acidobacteria and Parcubacteria in epiphytic biofilms; while 37 hubs from the 14 phyla (Proteobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, et al.) were detected in deciduous layer sediments. Our results indicate that bacterial community in deciduous layer sediments was more susceptible than in epiphytic biofilms during decay process. These data highlight the role of microbial community in deciduous layer sediments on nutrients removal during H. verticillata decay and will provide useful information for wetland management.

The abundance of nirS-type denitrifiers and anammox bacteria in rhizospheres was affected by the organic acids secreted from roots of submerged macrophytes

Excessive nitrogen has been a global concern to cause lake eutrophication. The denitrification and anammox processes are considered to be effective biological pathways for nitrogen removal. Submerged macrophytes also play a key role in the nitrogen cycle of lakes. However, the mechanism of submerged macrophytes on regulating biological nitrogen removal pathways has not been well quantified. Therefore, this study investigated the impacts of submerged macrophytes on the community structures and abundance of the nirS-type denitrifiers and anammox bacteria in the rhizospheres. The qPCR results indicated that the abundance of two bacteria in the near-rhizospheres of submerged macrophytes was significantly lower than the root compartments and non-rhizospheres, while the concentrations of organic acids in the near-rhizospheres were higher than those of the root compartments and non-rhizospheres. Redundancy analysis results illustrated that concentrations of NO₃^--N, NO₂^--N, citric acid and oxalic acid were the key environmental indicators which had the significant impact on the microbial community. The concentrations of citric acid and oxalic acid were negatively correlated with the nirS-type denitrifiers abundance, and the oxalic acid concentrations were negatively correlated with the anammox bacteria abundance. These results indicated that submerged macrophytes could reduce the abundance of nirS-type denitrifiers and anammox bacteria by releasing organic acids. In addition, the highest diversity of denitrifier community were found in the rhizosphere of the Hydrilla verticillata, while the highest diversity of anammox community were found in the Potamogeton maackianus rhizosphere. These results indicate that the impacts of submerged macrophytes on the biological nitrogen removal pathways were species-dependent.

The Water Hyacinth Microbiome: Link Between Carbon Turnover and Nutrient Cycling

Water hyacinth (WH), a large floating plant, plays an important role in the biogeochemistry and ecology of many freshwaters globally. Its biogeochemical impact on wetland functioning is strongly mediated by the microbiome associated with its roots. However, little is known about the structure and function of this WH rhizobiome and its relation to wetland ecosystem functioning. Here, we unveil the core and transient rhizobiomes of WH and their key biogeochemical functions in two of the world's largest wetlands: the Amazon and the Pantanal. WH hosts a highly diverse microbial community shaped by spatiotemporal changes. Proteobacteria lineages were most common, followed by Actinobacteria and Planctomycetes. Deltaproteobacteria and Sphingobacteriia predominated in the core microbiome, potentially associated with polysaccharide degradation and fermentation of plant-derived carbon. Conversely, a plethora of lineages were transient, including highly abundant Acinetobacter, Acidobacteria subgroup 6, and methanotrophs, thus assuring diverse taxonomic signatures in the two different wetlands. Our findings point out that methanogenesis is a key driver of, and proxy for, community structure, especially during seasonal plant decline. We provide ecologically relevant insights into the WH microbiome, which is a key element linking plant-associated carbon turnover with other biogeochemical fluxes in tropical wetlands.

The responding and ecological contribution of biofilm-leaves of submerged macrophytes on phenanthrene dissipation in sediments

The bacterial communities and ecological contribution of biofilm-leaves of the Vallisneria natans (VN), Hydrilla verticillata (HV) and artificial plant (AP) settled in sediments with different polluted levels of phenanthrene were investigated by high-throughput sequencing in different growth periods. There was no significant difference among the detected Alpha diversity indices based on three classification, attached surface, spiking concentration and incubation time. While Beta diversity analysis assessed by PCoA on operational taxonomic units (OTU) indicated that bacterial community structures were significantly influenced in order of attached surface > incubation time > spiking concentration of phenanthrene in sediment. Moreover, the results of hierarchical dendrograms and heat maps at genus level were consistent with PCoA analysis. We speculated that the weak influence of phenanthrene spiking concentration in sediment might be related to lower concentration and smaller concentration gradient of phenanthrene in leaves. Meanwhile, difference analysis suggested that attached surface was inclined to influence the rare genera up to significant level than incubation time. In general, the results proved that phenanthrene concentrations, submerged macrophytes categories and incubation time did influence the bacterial community of biofilm-leaves. In turn, results also showed a non-negligible ecological contribution of biofilm-leaves in dissipating the phenanthrene in sediments (>13.2%-17.1%) in contrast with rhizosphere remediation (2.5%-3.2% for HV and 9.9%-10.6% for VN).

Bacterial diversity and community structure during fermentation of Chinese sauerkraut with Lactobacillus casei 11MZ-5-1 by Illumina Miseq sequencing

The bacterial diversity and community structure involved in Chinese sauerkraut is one of the most important factors shaping the final characteristics of traditional foods. In this research, Lactobacillus casei 11MZ-5-1 was applied in Chinese sauerkraut fermentation as a starter culture. Illumina Miseq sequencing analysis was used to reveal the bacterial diversity and community structure during Chinese sauerkraut fermentation. A total of 177 283 high-quality reads of 16S rRNA V4 regions were obtained. The inoculation of L. casei 11MZ-5-1 decreased considerably the bacterial richness and bacterial diversity. This inoculum led to the replacement of Lactococcus by Lactobacillus. The levels of Pseudomonas and Enterobacter bacteria decreased. These findings reveal the evolution of important bacterial groups that are involved in fermentation and will facilitate improvements in the Chinese sauerkraut fermentation process.

SIGNIFICANCE AND IMPACT OF THE STUDY

This research thoroughly revealed the effects of Lactobacillus casei 11MZ-5-1 starter cultures on bacterial communities during Chinese sauerkraut fermentation. Illumina Miseq sequencing was effective technique to monitor the bacterial diversity and community structure. The inoculation of L. casei 11MZ-5-1 led to the decline of bacterial richness and diversity together with a consistent predominance of Lactobacillus during spontaneous fermentation. The result collectively suggested L. casei 11MZ-5-1 is a promising starter in Chinese sauerkraut manufacturing.