Sediment Biofilm Research Articles

Microbial Life in Playa-Lake Sediments: Adapted Structure, Plastic Function to Extreme Water Activity Variations

Saline shallow lakes in arid and semi-arid regions frequently undergo drying episodes, leading to significant variations in salinity and water availability. Research on the impacts of salinity and drought on the structure and function of biofilms in hypersaline shallow lakes is limited. This study aimed to understand the potential changes of biofilms in playa-lake sediments during the drying process. Sediments were sampled at different depths (surface, subsurface) and hydrological periods (wet, retraction, and dry), which included a decrease in water activity (aw, the availability of water for microbial use) from 0.99 to 0.72. aw reduction caused a greater effect on functional variables compared to structural variables, indicating the high resistance of the studied biofilms to changes in salinity and water availability. Respiration and hydrolytic extracellular enzyme activities exhibited higher values under high aw, while phenol oxidase activity and prokaryote biomass increased at lower aw. This shift occurred at both depths but was more pronounced at the surface, possibly due to the more extreme conditions (up to 0.7 aw). The increased levels of extracellular polymeric substances and carotenoids developed at low aw may help protect microorganisms in high salinity and drought environments. However, these harsh conditions may interfere with the activity of hydrolytic enzymes and their producers, while promoting the growth of resistant prokaryotes and their capacity to obtain C and N sources from recalcitrant compounds. The resilience of biofilms in hypersaline lakes under extreme conditions is given by their resistant biochemichal structure and the adaptability of their microbial functioning.

Interactions between water quality and microbes in epiphytic biofilm and superficial sediment of lake in trophic agriculture area

Epiphytic and superficial sediment biofilm-dwelling microbial communities play a pivotal role in water quality regulation and biogeochemical cycling in shallow lakes. However, the interactions are far from clear between water physicochemical parameters and microbial community on aquatic plants and in surface sediments of lake in trophic agriculture area. This study employed Illumina sequencing, Partial Least Squares Path Modeling (PLS-PM), and physico-chemical analytical methods to explore the interactions between water quality and microbes (bacteria and eukaryotes) in three substrates of trophic shallow Lake Cyohoha North, Rwanda. The Lake Cyohoha was significantly polluted with total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (NO3-N), and ammonia nitrogen (NH3−N) in the wet season compared to the dry season. PLS-PM revealed a strong positive correlation (+0.9301) between land use types and physico-chemical variables in the rainy season. In three substrates of the trophic lake, Proteobacteria, Cyanobacteria, Firmicutes, and Actinobacteria were dominant phyla in the bacterial communities, and Rotifers, Platyhelminthes, Gastrotricha, and Ascomycota dominated in microeukaryotic communities. As revealed by null and neutral models, stochastic processes predominantly governed the assembly of bacterial and microeukaryotic communities in biofilms and surface sediments. Network analysis revealed that the microbial interconnections in Ceratophyllum demersum were more stable and complex compared to those in Eichhornia crassipes and sediments. Co-occurrence network analysis (|r| > 0.7, p < 0.05) revealed that there were complex interactions among physicochemical parameters and microbes in epiphytic and sediment biofilms, and many keystone microbes on three substrates played important role in nutrients removal, food web and microbial community stable. These findings emphasize that eutrophic water influence the structure, composition, and interactions of microbes in epiphytic and surface sediment biofilms, and provided new insights into the interconnections between water quality and microbial community in presentative substrates in tropical lacustrine ecosystems in agriculturally polluted areas. The study provides useful information for water quality protection and aquatic plants restoration for policy making and catchment management.

Spatio-temporal variation of bacterial community structure in two intertidal sediment types of Jiaozhou Bay

The intertidal sediment environment is dynamic and the biofilm bacterial community within it must constantly adapt, but an understanding of the differences in the biofilm bacterial community within sediments of different types is still relatively limited. The semi-enclosed Jiaozhou Bay has a temperate monsoon climate, with strong currents at the mouth of the bay. In this study, the structure of the bacterial community in Jiaozhou Bay sediment biofilms are described using high-throughput 16 S rRNA gene sequencing and the effects of temporal change and different sediment environment types are discussed. Alpha diversity was significantly higher in sandy samples than in muddy samples. Sandy sediments with increased heterogeneity promote bacterial aggregation. Beta diversity analysis showed significant differences between sediment types and between stations. Proteobacteria and Acidobacteria were significantly more abundant at ZQ, while Campilobacterota was significantly more abundant at LC. The relative abundances of Bacteroidetes, Campilobacterota, Firmicutes, and Chloroflexi were significantly higher in the muddy samples, while Actinobacteria and Proteobacteria were higher in the sandy samples. There were different phylum-level biomarkers between sediment types at different stations. There were also different patterns of functional enrichment in biogeochemical cycles between sediment types and stations with the former having more gene families that differed significantly, highlighting their greater role in determining bacterial function. Bacterial amplicon sequence variant variation between months was less than KEGG ortholog variation between months, presumably the temporal change had an impact on shaping the intertidal sediment bacterial community, although this was less clear at the gene family level. Random forest prediction yielded a combination of 43 family-level features that responded well to temporal change, reflecting the influence of temporal change on sediment biofilm bacteria.

Presence of Leptospira spp. in a Mosaic of Wetlands Used for Livestock Raising under Differing Hydroclimatic Conditions.

Knowledge about the life cycle and survival mechanisms of leptospires in the environment is scarce, particularly regarding the environmental factors associated with their presence in ecosystems subject to livestock farming, where precipitation, seasonal floods, and river overflows could act as facilitators of leptospire dispersion. This study aimed to identify and study the presence of Leptospira spp. in the Lower Delta of the Paraná River and describe the physical, chemical, and hydrometeorological conditions associated with their presence in wetland ecosystems impaired by livestock raising intensification. Here, we show that the presence of Leptospira was determined mainly by water availability. We detected the species Leptospira kmetyi, L. mayottensis, and L. fainei and successfully cultured the saprophytic species L. meyeri from bottom sediment, suggesting the association of leptospires with microbial communities of the sediment's biofilm to enhance its survival and persistence in aquatic environments and adapt to changing environmental conditions. Knowledge of Leptospira sp. diversity in wetlands and the impact of climate variability on the transmission of these organisms is crucial for predicting and preventing leptospirosis outbreaks in the context of human health. IMPORTANCE Wetlands are environments that are often conducive to the survival and transmission of Leptospira because they provide a suitable habitat for the bacteria and are often home to many animal species that can act as reservoirs for leptospirosis. Bringing humans and animals into closer contact with contaminated water and soil and increased frequency and intensity of extreme weather events may further exacerbate the risk of leptospirosis outbreaks, which is mostly relevant in the context of climate change and a widespread intensification of productive activities, particularly in the Lower Delta of the Paraná River. The detection of leptospiral species in wetland ecosystems impaired by livestock raising intensification can help to identify propitious environmental factors and potential sources of infection, develop preventive measures, and plan for appropriate responses to outbreaks, ultimately improving public health outcomes.

Ocean acidification alters the benthic biofilm communities in intertidal soft sediments

Microphytobenthos (MPB) and bacterial biofilms play crucial roles in primary and secondary production, nutrient cycling and invertebrate settlement in coastal ecosystems, yet little is known of the effects of ocean acidification (OA) on these communities in intertidal soft sediments. To fill in this gap, a 28-day CO2 enhancement experiment was conducted for the benthic biofilms in soft intertidal sediments (muds and sands) from Qingdao, China. This experiment included three CO2 treatments: 400 ppm CO2 (control), 700 ppm CO2 and 1000 ppm CO2 (IPCC predicted value in 2100), which were established in a three-level CO2 incubator that can adjust the CO2 concentration in the overlying air. The effects of OA on benthic biofilms were assessed in the following three aspects: MPB biomass, biofilm community structure and microbial biogeochemical cycling (e.g., C-cycle, N-cycle and S-cycle). This study found that the 700 ppm CO2 treatment did not significantly affect the benthic biofilms in intertidal soft sediments, but the 1000 ppm CO2 treatment significantly altered the biofilm community composition and potentially their role in microbial biogeochemical cyc\ling in sediments (especially in sandy sediments). For the bacterial community in biofilms, the 1000 ppm CO2 enhancement increased the relative abundance of Alteromonadales and Bacillales but decreased the relative abundance of Rhodobacterales and Flavobacteriales. For microbial biogeochemical cycling, the 1000 ppm CO2 treatment enhanced the potential of chemoheterotrophic activity, nitrate reduction and sulfur respiration in sediments, likely resulting in a more stressful environment (hypoxic and enriched H2S) for most benthic organisms. Even though incubations in this study were only 28 days long and thus couldn’t fully accommodate the range of longer-term adaptions, it still suggests that benthic biofilms in intertidal sandy sediments are likely to change significantly near the end of the century if anthropogenic CO2 emissions unmitigated, with profound implications on local ecosystems and biogeochemical cycling.

Characterization of benthic biofilms in mangrove sediments and their variation in response to nutrients and contaminants.

Diatom-dominated biofilms and associated extracellular polymeric substances (EPS) may adapt to the stress of long-term exposure to nutrients and anthropogenic contaminants. However, such interactions in contaminated mangrove sediments have rarely been reported. Based on the in situ characterization of biofilm components and environmental factors, the present study aimed to explore the key factors involved in shaping sediment biofilms through correlational and multivariate analyses. The pennate diatom Navicula is the core taxon that plays a crucial role in balancing the abundance of Nitzschia and Cyclotella, and is the main producer of bound-polysaccharides. The taxa composition shifts in a high N/P matrix, with the populations of pennate diatoms increasing but that of centric diatoms decreasing. High nutrient concentrations yield more number of diatoms and elevated levels of EPS. Bacteria are the main consumers of EPS and tend to be more symbiotic with Nitzschia than the other two diatom taxa. Some bound-polysaccharides dominated by arabinose and glucose units are transformed into the colloidal fraction, whereas other conservative ones serve as structural materials in concert with the bound-proteins. The planktonic phase of Cyclotella breaks down the structural EPS secreted by pennate diatoms in a process that directly affects the dynamic renewal of benthic biofilms. Most heavy metals as well as bisphenol A inhibit the abundance of bacteria and diatoms but enhance most EPS fractions except bound-polysaccharides. The response of structural EPS to specific contaminants varies, exhibiting increases in Co and Ni levels but decreases in nonylphenol and methylparaben levels. The present study improves our understanding of the microbial carbon loop of benthic biofilms in mangrove ecosystems under stress by nutrients and mixed contaminants.

Trivalent iron shaped the microbial community structure to enhance the electrochemical performance of microbial fuel cells inoculated with soil and sediment

Bioelectrochemical performance of bacterial communities of cropland soil and lake sediment was evaluated in double chamber microbial fuel cells (MFCs) under the effect of trivalent iron [Fe(III)]. The MFCs were operated in a fed batch mode and their voltage output was measured for a period of 40 days. The highest outputs recorded under untreated conditions using cropland soil and lake sediment were 154 mV (current density= 0.06 mAcm−2, power density = 9.5 mWcm−2) and 137 mV (current density; 0.06 mAcm−2, power density; 7.5 mWcm−2), respectively. An about 87.7% (voltage; 289 mV, power density; 33.4 mWcm−2) and 45% (voltage: 160 mV, current density; 0.06 mAcm−2, power density; 10.24 mWcm−2) increase in voltage output was measured in the respective soil and sediment inoculated MFCs under iron treatment. The COD removal rate increased from 40% and 35–69% and 65% under treated conditions. Alpha rarefaction curves and Shannon index revealed soil derived biofilms contained the most diverse bacterial communities and diversity significantly reduced in sediment biofilm treated with Fe3+. Illumina MiSeq sequencing and scanning electron microscopy indicated the presence of a diverse microbial diversity where Proteobacteria, Bacteriodetes and Firmicutes were the most abundant phyla. Predominant genera included Pseudomonas, Sedimentibacter, Aminobacterium, Clostridium and Flavobacterium sp. MFCs with sediment supported the delta-proteobacteria; the class that includes Shewanella sp. and Geobacter sp., higher in the presence of Fe3+ than soil-MFCs. Based on 16SrRNA sequencing, isolated bacteria were identified as Staphylococcus sp., Bacillus sp., Streptomyces sp. and Gordonia sp., already reported for their electricity generation potential.

Exploring microbial diversity and ecological function of epiphytic and surface sediment biofilm communities in a shallow tropical lake

Microbial communities in epiphytic biofilms and surface sediments play a vital role in the biogeochemical cycles of the major chemical elements in freshwater. However, little is known about the diversity, composition, and ecological functions of microbial communities in shallow tropical lakes dominated by aquatic macrophytes. In this study, epiphytic bacterial and eukaryotic biofilm communities on submerged and floating macrophytes and surface sediments were investigated in Lake Rumira, Rwanda in August and November 2019. High-throughput sequencing data revealed that members of the phyla, including Firmicutes, Proteobacteria, Cyanobacteria, Actinobacteria, Chloroflexi, Bacteriodetes, Verrumicrobia, and Myxomycota, dominated bacterial communities, while the microeukaryotic communities were dominated by Unclassified (uncl) SAR(Stramenopiles, Alveolata, Rhizaria), Rotifers, Ascomycota, Gastrotricha, Platyhelminthes, Chloroplastida, and Arthropoda. Interestingly, the eukaryotic OTUs (operational taxonomic units) number and Shannon indices were significantly higher in sediments and epiphytic biofilms on Eicchornia crassipes than Ceratophyllum demersum (p < 0.05), while no differences were observed in bacterial OTUs number and Shannon values among substrates. Redundancy analysis (RDA) showed that water temperature, pH, dissolved oxygen (DO), total nitrogen (TN), and electrical conductivity (EC) were the most important abiotic factors closely related to the microbial community on C. demersum and E. crassipes. Furthermore, co-occurrence networks analysis (|r| > 0.7, p < 0.05) and functional prediction revealed more complex interactions among microbes on C. demersum than on E. crassipes and sediments, and those interactions include cross-feeding, parasitism, symbiosis, and predatism among organisms in biofilms. These results suggested that substrate-type and environmental factors were the strong driving forces of microbial diversity in epiphytic biofilms and surface sediments, thus shedding new insights into microbial community diversity in epiphytic biofilms and surface sediments and its ecological role in tropical lacustrine ecosystems.

A Win-Loss Interaction on Fe0 Between Methanogens and Acetogens From a Climate Lake.

Diverse physiological groups congregate into environmental corrosive biofilms, yet the interspecies interactions between these corrosive physiological groups are seldom examined. We, therefore, explored Fe0-dependent cross-group interactions between acetogens and methanogens from lake sediments. On Fe0, acetogens were more corrosive and metabolically active when decoupled from methanogens, whereas methanogens were more metabolically active when coupled with acetogens. This suggests an opportunistic (win–loss) interaction on Fe0 between acetogens (loss) and methanogens (win). Clostridia and Methanobacterium were the major candidates doing acetogenesis and methanogenesis after four transfers (metagenome sequencing) and the only groups detected after 11 transfers (amplicon sequencing) on Fe0. Since abiotic H2 failed to explain the high metabolic rates on Fe0, we examined whether cell exudates (spent media filtrate) promoted the H2-evolving reaction on Fe0 above abiotic controls. Undeniably, spent media filtrate generated three- to four-fold more H2 than abiotic controls, which could be partly explained by thermolabile enzymes and partly by non-thermolabile constituents released by cells. Next, we examined the metagenome for candidate enzymes/shuttles that could catalyze H2 evolution from Fe0 and found candidate H2-evolving hydrogenases and an almost complete pathway for flavin biosynthesis in Clostridium. Clostridial ferredoxin-dependent [FeFe]-hydrogenases may be catalyzing the H2-evolving reaction on Fe0, explaining the significant H2 evolved by spent media exposed to Fe0. It is typical of Clostridia to secrete enzymes and other small molecules for lytic purposes. Here, they may secrete such molecules to enhance their own electron uptake from extracellular electron donors but indirectly make their H2-consuming neighbors—Methanobacterium—fare five times better in their presence. The particular enzymes and constituents promoting H2 evolution from Fe0 remain to be determined. However, we postulate that in a static environment like corrosive crust biofilms in lake sediments, less corrosive methanogens like Methanobacterium could extend corrosion long after acetogenesis ceased, by exploiting the constituents secreted by acetogens.

An Untargeted Metabolomic Approach for Microphytobenthic Biofilms in Intertidal Mudflats

Microphytobenthic (MPB) biofilms in intertidal muddy sediments play important ecological functions in coastal ecosystems. These biofilms are mainly composed of epipelic diatoms but also prokaryotes, with a dominance of bacteria, which excrete diverse extracellular polymeric substances (EPS) according to their environment. While numerous studies have investigated the main components of these EPS matrices via traditional colorimetric assays, their fine composition, notably in specialized metabolites, is still largely unknown. A better chemical characterization of these MPB biofilms is necessary, especially regarding the numerous functions their chemical components play for microorganisms (e.g. motility, cell protection, defense mechanisms, chemical communication), but also for coastal systems (e.g. primary production, sediment stabilization, larval settlement of some invertebrates with high economical value). An alternative approach to traditional analyses is the use of untargeted metabolomic techniques, which have not yet been applied to such MPB biofilms. The objectives of the present study were to (a) propose a protocol for metabolic fingerprinting by LC-MS and GC-MS for metabolites analysis in polar and non-polar fractions in MPB biofilms extracted from mudflat sediment and to (b) apply this protocol to a case study: the effect of light exposure on the metabolomic fingerprint of the MPB biofilm community. We compared three extraction methods using different mixes of solvents and selected a methanol/chloroform mix (1:1), which gave better results for both techniques and fractions. We then applied the selected protocol to our case study using a short-term light exposure experiment in aquaria (7 days). The present study is the first using a detailed untargeted metabolomic approach on MPB biofilms from mudflat sediment and will provide a solid baseline for further work in this area

Alpine headwaters emerging from glaciers and rock glaciers host different bacterial communities: Ecological implications for the future

Mountain glacier shrinkage represents a major effect of the current global warming and 80–100% of the Alpine glaciers are predicted to vanish within the next few decades. As the thawing rate of mountain permafrost ice is much lower than for glacier ice, a shift from glacial to periglacial dynamics is predicted for Alpine landscapes during the 21st century. Despite the growing literature on the impacts of deglaciation on Alpine hydrology and ecosystems, chemical and biological features of waters emerging from Alpine rock glaciers (i.e. permafrost landforms composed by a mixture of ice and debris) have been poorly investigated so far, and knowledge on microbial biodiversity of headwaters is still sparse. A set of glacier-, rock glacier- and groundwater/precipitation-fed streams was investigated in the Italian Central Alps in late summer 2016, aiming at exploring bacterial community composition and diversity in epilithic and surface sediment biofilm and at verifying the hypothesis that rock glacier-fed headwaters represent peculiar ecosystems from both a chemical and biological point of view. Rock glacier-fed waters showed high values of electrical conductivity and trace elements related to their bedrock lithology, and their highly diverse bacterial assemblages significantly differed from those detected in glacier-fed streams. Bacterial taxonomic composition appeared to be mainly related to water and substrate type, as well as to water chemistry, the latter including concentrations of nutrients and trace metals. The results of this study confirm the chemical and biological peculiarity of rock glacier-fed waters compared to glacial waters, and suggest a potential driving role of thawing permafrost in modulating future ecological traits of Alpine headwaters within the context of progressing deglaciation.

Evaluating the Impact of Wastewater Effluent on Microbial Communities in the Panke, an Urban River

Pharmaceuticals are consumed in high amounts and can enter as emerging organic compounds in surface waters as they are only partially retained in wastewater treatment plants (WWTPs). Receiving pharmaceuticals may burden the aquatic environment, as they are designed to be bioactive even at low concentrations. Sediment biofilm populations were analyzed in river sediments due to the exposure of an inflow of WWTP effluents. Illumina MiSeq 16S rRNA gene amplicon sequencing was performed of 108 sediment samples, which were taken from multiple cores within three sampling locations in the Panke River, with one sampling site located downstream of the inflow. Sequencing data were processed to infer microbial community structure in samples concerning the environmental variables, such as micropollutants and physicochemical parameters measured for each core. More than 25 different micropollutants were measured in pore water samples, in which bezafibrate, clofibric acid, carbamazepine, and diclofenac were detected at high concentrations. Bacterial 16S rRNA gene amplicons revealed Nitrospirae, Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Bacteroidetes, and Ignavibacteriae as the most abundant groups in the samples. Differences in microbial community composition were observed with respect to micropollutants. However, our findings revealed that the composition of the microbial community was not only governed by the effluent. The significant changes in the alpha- and beta-diversity were explained by phenobarbital and SO42−, which did not originate from the WWTP indicating that more unobserved factors are also likely to play a role in affecting the biofilm community’s composition.

Low concentrations of copper oxide nanoparticles alter microbial community structure and function of sediment biofilms

In this study, we investigated the effects of copper oxide (CuO) NPs on freshwater sediment biofilms in terms of the functional properties and microbial community structure. Biofilms were incubated in microcosms and CuO NPs (1 mg/L uncoated and humic-acid-coated) were exposed with Cu2+ (Cu(NO3)2) as the positive control. As determined from DO (dissolved oxygen) microelectrodes measurements, a high-DO region emerged inside the biofilms after 5-day exposure to CuO NPs compared with those before NP additions, which suggested CuO NPs inhibit the oxygen respiration activity. These results were consistent with the decreased heterotrophic respiration. CuO NPs significantly altered the bacterial community composition and decreased the abundances of Anaerolineaceae, Acidobacteria, Aminicenantes, and Anaerolinea. Functional analysis from PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States)-predicted metagenomes indicated that bacterial genera depleted by CuO NP treatments were related to carbohydrate and glycan biosynthesis and metabolism, and biosynthesis of other secondary metabolites. These functional profiles combined with the decreased activities of extracellular enzymes, β-glucosidase (GLU) and l-leucine aminopeptidase (LAP), suggested that the introduction of CuO NPs exhibit negative effects on the biogeochemical processes and the cycling of carbon and nitrogen in biofilm systems. Whereas these toxic effects of CuO NPs could be mitigated when the aquatic environment is enriched with natural organic matters such as humic acid.

Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments.

ABSTRACTSubsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.

Effect of particle size and heterogeneity on sediment biofilm metabolism and nutrient uptake scaled using two approaches

AbstractNumerous studies have examined the effect of sediment particle size and distribution on community structure, but few have focused explicitly on how physical habitat characteristics influence biogeochemical functions of freshwater biofilms. In this study, we evaluated the effect of particle size and heterogeneity on rates of biofilm metabolism and nutrient uptake in colonized and native sediments normalized using two different scaling approaches. Coarse, pebble‐ to cobble‐sized sediments were sorted into four homogeneous particle size treatments plus one heterogeneous treatment. Each treatment was deployed, in replicate, within one riffle and one run habitat feature in three different high‐latitude stream reaches with contrasting hydrological and physicochemical characteristics. A treatment of native, homogeneous sediment was also evaluated at each deployment location. After incubating for approximately five weeks, metabolism and nutrient uptake of biofilms in all treatments (n = 69) were measured in recirculating microcosm chambers. For each treatment, functional rates were normalized by projected surface area and sediment surface area scaling approaches, which account for the surface area in plan view (looking top‐down) and the total surface area of all sediment particles, respectively. This comparison was designed to determine whether treatment effects were independent of increased surface area associated with smaller particle sizes or heterogeneous sediments. Community respiration and uptake of ammonium‐nitrogen and phosphate‐phosphorus by biofilms decreased significantly as the particle size of homogeneous treatments increased when normalized by projected surface area, but significantly increased with increasing particle size when normalized by sediment surface area. Sediment particle size had a limited influence on production rates evaluated across treatments. Heterogeneous and homogeneous treatments with similar median particle sizes did not differ significantly from one another for most biogeochemical functions measured. Our findings indicate that rates of biogeochemical function in heterogeneous habitats were directly related to the total sediment surface area available for biofilm colonization. The significant interactions between sediment surface area and rates of respiration and nutrient uptake suggest that information about the size and distribution of sediment particles could substantially improve our ability to predict and scale measurements of important biogeochemical functions in streams.

Diatom species variation between lake habitats: implications for interpretation of paleolimnological records

A sample of a sediment record contains diatom species that have grown in disparate habitats and eventually accumulated in a deep part of the lake. The original habitats may differ in substrate, depth location, and availability of resources. Identifying the species characteristic of each habitat should improve our ecological and environmental interpretation of the sediment record by distinguishing habitat specific responses. With this aim, we studied the benthic diatom communities of a deep oligotrophic lake across several habitats. The main source of variation in the diatom composition was the substrate type; particularly, sediment biofilms. Depth was the second factor. The thermocline defined a shift in diatom communities that also included changes in the dominant lifeforms. A third factor was the mesoscale heterogeneity (i.e., rock sides). Although most species were present in many habitats, characteristic species were identified for all the main habitats and used for an improved interpretation of the deep sediment record. Appropriate standardization showed increasing species richness and diversity from epilimnetic epilithic samples to hypolimnetic sediment samples. We estimate that more than 5000 valve counts are required for appropriate comparisons. Consequently, in sediment records with lower counts per sample, one has to amalgamate samples—losing temporal resolution—to achieve reliable analyses of diversity changes over time. Deep sediment samples are representative of the gamma-diversity of the lake diatom metacommunity, which result from the local alpha diversity of the habitats and the beta-diversity of the variability in composition among them. This double source of diversity has to be taken into account when using the sediment record for estimating lake biodiversity changes. On the other hand, we show that an estimation of the spatial (habitat) heterogeneity of a reconstructed environmental variable can be achieved using subsets of species characteristic of each habitat. We demonstrate the procedure by reconstructing the pH fluctuations during the last 200 years in several habitats from a single sediment record. The results are coherent with the expected differences between predominantly trophogenic or tropholithic habitats.

Overproduction of microbial extracellular polymeric substances in subtropical intertidal sediments in response to endocrine disrupting chemicals

Microorganisms and their extracellular polymeric substances (EPS) in sediments are important in sediment stabilization and the fate of pollutants. However, how toxic organic pollutants affect bacteria and EPS in sediments, particularly in subtropical intertidal zones is poorly known. The present study aims to investigate the bacterial abundance and related EPS in simulated intertidal sandflat and mangrove sediments under the stress of endocrine disrupting chemicals (EDCs). Results showed that the temporal changes of the bacterial number in both sandflat and mangrove sediments were similar, increased from days 0 to 56 then became steady during the 84-days incubation. Bacteria exhibited an important role in the production of high molecular weight (HMW) EPS protein and the degradation of the low molecular weight (LMW) EPS protein. During incubation, the EPS polysaccharides changed from a colloidal-LMW fraction at the beginning to a more complex-HMW fraction at the end of the experiment. The increases in the concentration of HMW polysaccharides might contribute to sediment stabilization. Among different spiked EDCs, nonylphenol (NP) and 17α-ethinylestradiol (EE2) tended to accumulate in both sandflat and mangrove sediments and posed stresses to bacterial growth, especially the latter sediment. The persistent EDCs promoted a higher production of EPS polysaccharides and proteins in both sediments when compared to the respective control, but the EPS in the sandflat sediment was mainly in the colloidal fraction while the bound fraction was more abundant in the mangrove sediment. The present results enhance our understanding of the effects of EDCs on sediment biofilms in intertidal systems. This study also demonstrates the significance of EPS polysaccharides and proteins in sediment stabilization and provides a fundamental basis for future microbiology studies.

Underestimated effects of sediments on enhanced startup performance of biofilm systems for polluted source water pretreatment.

In order to evaluate the enhancement mechanisms of enhanced startup performance in biofilm systems for polluted source water pretreatment, three lab-scale reactors with elastic stereo media (ESM) were operated under different enhanced sediment and hydraulic agitation conditions. It is interesting to found the previously underestimated or overlooked effects of sediment on the enhancement of pollutants removal performance and enrichment of functional bacteria in biofilm systems. The maximum NH4+-N removal rate of 0.35mg L-1 h-1 in sediment enhanced condition was 2.19 times of that in control reactor. Sediment contributed to 42.0-56.5% of NH4+-N removal and 15.4-41.2% of total nitrogen removal in different reactors under different operation conditions. The enhanced hydraulic agitation with sediment further improved the operation performance and accumulation of functional bacteria. Generally, Proteobacteria (48.9-52.1%), Bacteroidetes (18.9-20.8%) and Actinobacteria (15.7-18.5%) were dominant in both sediment and ESM bioiflm at phylum level. The potentially functional bacteria found in sediment and ESM biofilm samples with some functional bacteria mainly presented in sediment samples only (e.g., Genera Bacillus and Lactococcus of Firmicutes phylum) may commonly contribute to the removal of nitrogen and organics.

Multiscale Investigation on Biofilm Distribution and Its Impact on Macroscopic Biogeochemical Reaction Rates

AbstractBiofilms are critical locations for biogeochemical reactions in the subsurface environment. The occurrence and distribution of biofilms at microscale as well as their impacts on macroscopic biogeochemical reaction rates are still poorly understood. This paper investigated the formation and distributions of biofilms in heterogeneous sediments using multiscale models and evaluated the effects of biofilm heterogeneity on local and macroscopic biogeochemical reaction rates. Sediment pore structures derived from X‐ray computed tomography were used to simulate the microscale flow dynamics and biofilm distribution in the sediment column. The response of biofilm formation and distribution to the variations in hydraulic and chemical properties was first examined. One representative biofilm distribution was then utilized to evaluate its effects on macroscopic reaction rates using nitrate reduction as an example. The results revealed that microorganisms primarily grew on the surfaces of grains and aggregates near preferential flow paths where both electron donor and acceptor were readily accessible, leading to the heterogeneous distribution of biofilms in the sediments. The heterogeneous biofilm distribution decreased the macroscopic rate of biogeochemical reactions as compared with those in homogeneous cases. Operationally considering the heterogeneous biofilm distribution in macroscopic reactive transport models such as using dual porosity domain concept can significantly improve the prediction of biogeochemical reaction rates. Overall, this study provided important insights into the biofilm formation and distribution in soils and sediments as well as their impacts on the macroscopic manifestation of reaction rates.

Enhancement of carbon and nitrogen removal by helophytes along subsurface water flowpaths receiving treated wastewater

Wastewater treatment plant (WWTP) effluents are sources of dissolved organic carbon (DOC) and inorganic nitrogen (DIN) to receiving streams, which can eventually become saturated by excess of DIN. Aquatic plants (i.e., helophytes) can modify subsurface water flowpaths as well as assimilate nutrients and enhance microbial activity in the rhizosphere, yet their ability to increase DIN transformation and removal in WWTP-influenced streams is poorly understood. We examined the influence of helophytes on DIN removal along subsurface water flowpaths and how this was associated with DOC removal and labile C availability. To do so, we used a set of 12 flow-through flumes fed with water from a WWTP effluent. The flumes contained solely sediments or sediments with helophytes. Presence of helophytes in the flumes enhanced both DIN and DOC removal. Experimental addition of a labile C source into the flumes resulted in a high removal of the added C within the first meter of the flumes. Yet, no concomitant increases in DIN removal were observed. Moreover, results from laboratory assays showed significant increases in the potential denitrifying enzyme activity of sediment biofilms from the flumes when labile C was added; suggesting denitrification was limited by C quality. Together these results suggest that lack of DIN removal response to the labile C addition in flumes was likely because potential increases in denitrification by biofilms from sediments were counterbalanced by high rates of mineralization of dissolved organic matter. Our results highlight that helophytes can enhance DIN removal in streams receiving inputs from WWTP effluents; and thus, they can become a relevant bioremediation tool in WWTP-influenced streams. However, results also suggest that the quality of DOC from the WWTP effluent can influence the N removal capacity of these systems.