Characterization of specificity of bacterial community structure within the burrow environment of the marine polychaete Hediste (Nereis) diversicolor

Bacterial community composition in the Northern Gulf of Mexico intertidal sediment bioturbated by the ghost shrimp Lepidophthalmus louisianensis

Bioturbation plays an important role in structuring microbial communities in coastal sediments. This study investigates the bacterial community composition in sediment associated with the ghost shrimp Lepidophthalmus louisianensis at two locations in the Northern Gulf of Mexico (Bay St. Louis, MS, and Choctawhatchee Bay, FL). Bacteria were analysed for shrimp burrows and for three different depths of bioturbated intertidal sediment, using second-generation sequencing of the 16S rRNA gene. Burrow walls held a unique bacterial community, which was significantly different from those in the surrounding sediment communities. Communities in burrow walls and surrounding sediment communities also differed between the two geographic locations. The burrow wall communities from both locations were more similar to each other than to sediment communities from same location. Alpha- and Gammaproteobacteria were more abundant in burrows and surface sediment than in the subsurface, whereas Deltaproteobacteria were more abundant in burrows and subsurface sediment, suggesting sediment mixing by the bioturbator. However, abundance of individual ASVs was geographic location-specific for all samples. Therefore, it is suggested that the geographic location plays an important role in regional microbial communities distinctiveness. Bioturbation appears to be an important environmental driver in structuring the community around burrows. Sampling was conducted during times of the year and water salinity, tidal regime and temperature were variable, nevertheless the structure microbial communities appeared to remain realatively stable suggesting that these environmental variable played only a minor role.

The Impact of Sea Ice Cover on Microbial Communities in Antarctic Shelf Sediments

The area around the Antarctic Peninsula (AP) is facing rapid climatic and environmental changes, with so far unknown impacts on the benthic microbial communities of the continental shelves. In this study, we investigated the impact of contrasting sea ice cover on microbial community compositions in surface sediments from five stations along the eastern shelf of the AP using 16S ribosomal RNA (rRNA) gene sequencing. Redox conditions in sediments with long ice-free periods are characterized by a prevailing ferruginous zone, whereas a comparatively broad upper oxic zone is present at the heavily ice-covered station. Low ice cover stations were highly dominated by microbial communities of Desulfobacterota (mostly Sva1033, Desulfobacteria, and Desulfobulbia), Myxococcota, and Sva0485, whereas Gammaproteobacteria, Alphaproteobacteria, Bacteroidota, and NB1-j prevail at the heavy ice cover station. In the ferruginous zone, Sva1033 was the dominant member of Desulfuromonadales for all stations and, along with eleven other taxa, showed significant positive correlations with dissolved Fe concentrations, suggesting a significant role in iron reduction or an ecological relationship with iron reducers. Our results indicate that sea ice cover and its effect on organic carbon fluxes are the major drivers for changes in benthic microbial communities, favoring potential iron reducers at stations with increased organic matter fluxes.

Bioturbation by the marine polychaete Capitella teleta alters the sediment microbial community by ingestion and defecation of sediment particles

Deposit-feeding benthic invertebrates are known to modify sediment structure and impact microbial processes associated with biogeochemical cycles in marine sedimentary environments. Despite this, however, there is limited information on how sediment ingestion and defecation by marine benthos alters microbial community structure and function in sediments. In the current study, we used high-throughput sequencing data of 16S rRNA genes obtained from a previous microcosm study to examine how sediment processing by the marine polychaete Capitella teleta specifically affects sediment microbiota. Here we show that both sediment ingestion and defecation by C. teleta significantly alters overall microbial community structure and function. Sediment processing by C. teleta resulted in significant enrichment of sediment microbial communities involved in sulfur and carbon cycling in worm fecal pellets. Moreover, C. teleta's microbiota was predominantly comprised of bacterial functional groups involved in fermentation, relative to microbiota found outside of the host. Collectively, results of this study indicate that C. teleta has the ability to alter microbial biogeochemical cycles in the benthic sedimentary environment by altering microbial assemblages in the worm gut, and in the sediment ingested and defecated by worms as they feed on sediment particles. In this sense, C. teleta plays an important role as an ecosystem engineer and in shaping nutrient cycling in the benthic environment.

The effect of bioturbation by polychaete Perinereis aibuhitensis on release and distribution of buried hydrocarbon pollutants in coastal muddy sediment

As a headdown deposit feeder, polychaete Perinereis aibuhitensis may transport particles from the deep sediment layers to the surface enhancing sediment resuspension, which influences the fate of sediment-associated pollutants. The impact of P. aibuhitensis on the remobilization of buried hydrocarbons was investigated through a 30 day laboratory microcosm experiment with hydrocarbon spiked sediment buried in different layers. The bioturbation of P. aibuhitensis enhanced sediment resuspension by approximately fourfold suspended particulate matters (SPM) and twofold dissolved organic carbon (DOC) in bioturbation (BI) microcosms (added P. aibuhitensis) than control (CL) microcosms (without P. aibuhitensis). The release of buried hydrocarbons were also enhanced with significantly higher hydrocarbon concentrations in BI microcosms than CL and blank (BK) microcosms (without spiked hydrocarbons). The presence of P. aibuhitensis led to the transport of buried spiked hydrocarbons in sediment and enhanced the loss of buried hydrocarbons.

Enhanced removal of sediment-associated total petroleum hydrocarbons under bioturbation by polychaete perinereis aibuhitensis

Bioturbation processes could influence the physical, chemical and biological properties of aquatic sediments and improve the mineralization of organic matter in sediment. The influence of bioturbation by polychaete Perinereis aibuhitensis on the removal of sediment-associated total petroleum hydrocarbon (TPH) was evaluated through laboratory experiment with P. aibuhitensis cultured in crude oil contaminated coastal sediment. After 60 days, the TPH concentrations in the sediments were significantly decreased compared to the initial concentrations, in which the TPH concentrations in bioturbation experiments (with worms) were significantly lower than those in control experiments (without worms) for both low (1.48 ± 0.19g/kg dry wt) and high (2.67 ± 0.33 g/kg dry wt) TPH-contaminated groups, indicating bioturbation enhanced the removal of TPH in sediment. The TPH removal rates in high TPH group were significantly lower than those in low TPH group, suggested that petroleum pollution inhibited the degradation of petroleum hydrocarbons in sediment. However, the stimulation efficiency was higher in high TPH group than that in low TPH group, which may be the result of enhanced hydrocarbon's bioavailability by digestive fluid during gut transit.

Microbiomes of the Enteropneust, Saccoglossus bromophenolosus, and Associated Marine Intertidal Sediments of Cod Cove, Maine

Enteropneusts are widely distributed marine invertebrates that accumulate high concentrations of halogenated aromatics. Some of these compounds affect benthic biogeochemistery (e.g., denitrification and ammonia oxidation), but little is known about interactions between enteropneusts and their associated microbial communities. Even less is known about enteropneust host-microbe relationships in the digestive tract. More generally, microbial community composition and diversity in intertidal sediments have received little attention. In this study, high throughput sequence analyses of 16S rRNA genes extracted from microbial communities associated with sediment-free whole individuals of Saccoglossus bromophenolosus and freshly excreted S. bromophenolosus gut sediments revealed a potential Spirochaete symbiont that was abundant, present in gut sediment, but absent in other sediments. Relative to surface sediments, gut communities also revealed evidence for selective losses of some groups and blooms of others, especially Colwellia, Photobacterium, Pseudoalteromonas, and Vibrio. After deposition, gut sediment communities rapidly resembled those of surface sediments. Although hierarchical cluster analysis and Linear Discriminant Analysis Effect Size (LEfSe) differentiated among burrow walls of S. bromophenolosus and a polychaete, Alitta virens, as well as between surface and sub-surface sediments, most operational taxonomic units (OTUs) were shared, with differences largely occurring in relative abundances. This suggests that sediment mixing through bioturbation might act to homogenize community composition, while species-specific impacts by infauna might alter local population abundances. Although Cod Cove is a relatively isolated intertidal system, microbial community members included groups with cosmopolitan distributions and roles in sulfur cycling, e.g., Gammaproteobacteria BD7 and Sva0071, as well as novel OTUs representing a large number of phyla.

Influence of Macrofaunal Burrows on Extracellular Enzyme Activity and Microbial Abundance in Subtropical Mangrove Sediment

Bioturbation and bioirrigation induced by burrowing macrofauna are recognized as important processes in aquatic sediment since macrofaunal activities lead to the alteration of sediment characteristics. However, there is a lack of information on how macrofauna influence microbial abundance and extracellular enzyme activity in mangrove sediment. In this study, the environmental parameters, extracellular enzyme activities, and microbial abundance were determined and their relationships were explored. Sediment samples were taken from the surface (S) and lower layer (L) without burrow, as well as crab burrow wall (W) and bottom of crab burrow (B) located at the Mai Po Nature Reserve, Hong Kong. The results showed that the burrowing crabs could enhance the activities of oxidase and hydrolases. The highest activities of phenol oxidase and acid phosphatase were generally observed in B sediment, while the highest activity of N-acetyl-glucosaminidase was found in W sediment. The enzymatic stoichiometry indicated that the crab-affected sediment had similar microbial nitrogen (N) and phosphorous (P) availability relative to carbon (C), lower than S but higher than L sediment. Furthermore, it was found that the highest abundance of both bacteria and fungi was shown in S sediment, and B sediment presented the lowest abundance. Moreover, the concentrations of phosphorus and soluble phenolics in crab-affected sediment were almost higher than the non-affected sediment. The alterations of phenolics, C/P and N/P ratios as well as undetermined environmental factors by the activities of crabs might be the main reasons for the changes of enzyme activity and microbial abundance. Finally, due to the important role of phenol oxidase and hydrolases in sediment organic matter (SOM) decomposition, it is necessary to take macrofaunal activities into consideration when estimating the C budget in mangrove ecosystem in the future.

Assessment of mobilization of labile phosphorus and iron across sediment-water interface in a shallow lake (Hongze) based on in situ high-resolution measurement

The internal loading of P is reported to be the main factor initiating algal blooms. However, there are only a few reports on the dynamic variation of labile P in the sediment and overlying water during the decomposition of algal. In addition, the widely perceived relationship between labile P and Fe was not supported by in situ obtained values in freshwater. Consequently, the in situ simultaneous measurement of diffusion gradients in thin-film techniques (DGT) was applied on a large scale to detect the mechanisms of labile P and Fe in a typical shallow lake (Lake Hongze). The newly developed ZrO-DGT and ZrO-Chelex DGT were combined to obtain the concentration of labile P and Fe. Results showed that decomposition of algal might be the main contributor for the concentration dots and peaks of labile P in sediment profiles, as well as for the high values on the horizontal heterogeneity index of labile P at the depth of 0-30 mm of the sediment. Moreover, there existed significant difference between the apparent diffusion fluxes of labile P and Fe across the sediment-water interface which obtained from June sampling and October sampling. The results of apparent diffusion flux in two periods indicated the sediments changed from "sink" to "source" for labile P, especially at Sites 4-8, 10, 13-14, and 18. However, the role of the labile Fe has no significantly variation in the values of the diffusion flux. This phenomenon also contributed to the poor relationship between labile P and Fe in the sediment which obtained from the October sampling. Accordingly, we conclude that algal decomposition might be essential for internal loading of P in this aquatic ecosystem, and that also be the reason for vicious circle of algal occurrence in the following year in the center of Lake Hongze.

Metatranscriptomes of oil-contaminated marine coastal sediment affected by oil addition and/or by the bioturbating activity of the marine polychaete Hediste diversicolor: Who are the microbial players?

In coastal marine sediment, oxygen fluctuations induced by bioturbating activities are widespread and exert a great influence, not only on the structure and diversity of the microbenthic communities, but also on their activities. Thus, the activity of benthic organisms can have a significant influence on the degradation of hydrocarbons (HC) and can favor the development of hydrocarbonoclastic microorganisms in contaminated marine sediments. Here, we have generated metatranscriptomic data from coastal marine sediments affected by oil addition and/or by the reworking activity of the marine polychaete Hediste diversicolor to gain insights into the active microbial groups involved in the response to oil addition under the oxygen-fluctuating conditions. The preliminary results suggest that the macrofauna promote the diversity of active aerobic hydrocarbonoclastic bacteria in marine sediments, even if its influence cannot be strongly observed at the microbial community expression profiles level.

Coexistence of Microaerophilic, Nitrate-Reducing, and Phototrophic Fe(II) Oxidizers and Fe(III) Reducers in Coastal Marine Sediment

Iron is abundant in sediments, where it can be biogeochemically cycled between its divalent and trivalent redox states. The neutrophilic microbiological Fe cycle involves Fe(III)-reducing and three different physiological groups of Fe(II)-oxidizing microorganisms, i.e., microaerophilic, anoxygenic phototrophic, and nitrate-reducing Fe(II) oxidizers. However, it is unknown whether all three groups coexist in one habitat and how they are spatially distributed in relation to gradients of O2, light, nitrate, and Fe(II). We examined two coastal marine sediments in Aarhus Bay, Denmark, by cultivation and most probable number (MPN) studies for Fe(II) oxidizers and Fe(III) reducers and by quantitative-PCR (qPCR) assays for microaerophilic Fe(II) oxidizers. Our results demonstrate the coexistence of all three metabolic types of Fe(II) oxidizers and Fe(III) reducers. In qPCR, microaerophilic Fe(II) oxidizers (Zetaproteobacteria) were present with up to 3.2 × 10(6) cells g dry sediment(-1). In MPNs, nitrate-reducing Fe(II) oxidizers, anoxygenic phototrophic Fe(II) oxidizers, and Fe(III) reducers reached cell numbers of up to 3.5 × 10(4), 3.1 × 10(2), and 4.4 × 10(4) g dry sediment(-1), respectively. O2 and light penetrated only a few millimeters, but the depth distribution of the different iron metabolizers did not correlate with the profile of O2, Fe(II), or light. Instead, abundances were homogeneous within the upper 3 cm of the sediment, probably due to wave-induced sediment reworking and bioturbation. In microaerophilic Fe(II)-oxidizing enrichment cultures, strains belonging to the Zetaproteobacteria were identified. Photoferrotrophic enrichments contained strains related to Chlorobium and Rhodobacter; the nitrate-reducing Fe(II) enrichments contained strains related to Hoeflea and Denitromonas. This study shows the coexistence of all three types of Fe(II) oxidizers in two near-shore marine environments and the potential for competition and interrelationships between them.

Effect of physical sediments reworking on hydrocarbon degradation and bacterial community structure in marine coastal sediments

The present study aimed to examine whether the physical reworking of sediments by harrowing would be suitable for favouring the hydrocarbon degradation in coastal marine sediments. Mudflat sediments were maintained in mesocosms under conditions as closer as possible to those prevailing in natural environments with tidal cycles. Sediments were contaminated with Ural blend crude oil, and in half of them, harrowing treatment was applied in order to mimic physical reworking of surface sediments. Hydrocarbon distribution within the sediment and its removal was followed during 286 days. The harrowing treatment allowed hydrocarbon compounds to penetrate the first 6 cm of the sediments, and biodegradation indexes (such as n-C18/phytane) indicated that biodegradation started 90 days before that observed in untreated control mesocosms. However, the harrowing treatment had a severe impact on benthic organisms reducing drastically the macrofaunal abundance and diversity. In the harrowing-treated mesocosms, the bacterial abundance, determined by 16S rRNA gene Q-PCR, was slightly increased; and terminal restriction fragment length polymorphism (T-RFLP) analyses of 16S rRNA genes showed distinct and specific bacterial community structure. Co-occurrence network and canonical correspondence analyses (CCA) based on T-RFLP data indicated the main correlations between bacterial operational taxonomic units (OTUs) as well as the associations between OTUs and hydrocarbon compound contents further supported by clustered correlation (ClusCor) analysis. The analyses highlighted the OTUs constituting the network structural bases involved in hydrocarbon degradation. Negative correlations indicated the possible shifts in bacterial communities that occurred during the ecological succession.

Response of microbial communities to bioturbation by artificially introducing macrobenthos to mudflat sediments for in situ bioremediation in a typical semi-enclosed bay, southeast China

Although microbes play important roles during the bioremediation process using macrobenthos in degraded environments, their response to macrobenthos bioturbation remains poorly understood. This study used 16S rRNA gene-Illumina Miseq sequencing to investigate the microbial communities and their response to bioturbation by artificially introducing macrobenthos to the mudflat of Sansha Bay, southeast China. A total of 56 phyla were identified, dominated by δ- and γ-Proteobacteria, with a total percentage of over 50%. Others, such as Acidobacteria, Chloroflexi, Bacteroidetes, Planctomycetes and Alphaproteobacteria occupied 4-7% respectively. Eighteen genera indicating the microbial communities response to bioturbation and seasonal change were identified. Bioturbated samples contained more ecologically important genera, and untreated samples contained more genera ubiquitous in marine environments. The physicochemical characteristics did not change significantly probably due to the short time of bioremediation and low survival rate of macrobenthos, confirming that microbial communities are more sensitive and can serve as sentinels for environmental changes.

Effects of benthic macrofauna bioturbation on the bacterial community composition in lake sediments

Benthic macrofauna are considered to be an important part of the lacustrine ecosystem, and bioturbation may greatly affect the biogeochemical processes and microbial activities in sediments. In the present study, the bacterial community composition in sediments inhabited by 3 different types of benthic macrofauna (Corbicula fluminea, Chironomidae larvae, and tubificid worms) in the shallow and eutrophic Lake Taihu was studied to investigate the different effects of bioturbation on the composition of these communities. Microcosms were constructed, and culture-independent methods, including terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis, were performed to evaluate the bacterial communities. Analysis of similarities (ANOSIM) and multidimensional scaling (MDS) analysis of T-RFLP patterns demonstrated that differences in the bacterial community composition between the control and the macrofauna-inhabited sediments were not as great as expected, although the chemical properties of the sediments changed remarkably. Nevertheless, the dominant bacterial group in each type of macrofauna-inhabited sediment was different. Acidobacteria, Betaproteobacteria, and Deltaproteobacteria were the dominant bacterial groups in sediments inhabited by C. fluminea, tubificid worms, and Chironomidae larvae, respectively. The data obtained in this study are helpful for understanding the effects of bioturbation in a shallow, eutrophic lake.