Benthic Biofilms Research Articles

Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function.

The shrinking of glaciers is among the most iconic consequences of climate change. Despite this, the downstream consequences for ecosystem processes and related microbiome structure and function remain poorly understood. Here, using a space‐for‐time substitution approach across 101 glacier‐fed streams (GFSs) from six major regions worldwide, we investigated how glacier shrinkage is likely to impact the organic matter (OM) decomposition rates of benthic biofilms. To do this, we measured the activities of five common extracellular enzymes and estimated decomposition rates by using enzyme allocation equations based on stoichiometry. We found decomposition rates to average 0.0129 (% d−1), and that decreases in glacier influence (estimated by percent glacier catchment coverage, turbidity, and a glacier index) accelerates decomposition rates. To explore mechanisms behind these relationships, we further compared decomposition rates with biofilm and stream water characteristics. We found that chlorophyll‐a, temperature, and stream water N:P together explained 61% of the variability in decomposition. Algal biomass, which is also increasing with glacier shrinkage, showed a particularly strong relationship with decomposition, likely indicating their importance in contributing labile organic compounds to these carbon‐poor habitats. We also found high relative abundances of chytrid fungi in GFS sediments, which putatively parasitize these algae, promoting decomposition through a fungal shunt. Exploring the biofilm microbiome, we then sought to identify bacterial phylogenetic clades significantly associated with decomposition, and found numerous positively (e.g., Saprospiraceae) and negatively (e.g., Nitrospira) related clades. Lastly, using metagenomics, we found evidence of different bacterial classes possessing different proportions of EEA‐encoding genes, potentially informing some of the microbial associations with decomposition rates. Our results, therefore, present new mechanistic insights into OM decomposition in GFSs by demonstrating that an algal‐based “green food web” is likely to increase in importance in the future and will promote important biogeochemical shifts in these streams as glaciers vanish.

The Resilience of Biofilm‐Bound Sandy Systems to Cyclic Changes in Shear Stress

AbstractSand‐attached benthic biofilms drive many important biogeological processes and serve as cooperative “ecosystem engineers”. In aquatic environments, biofilms undergo periodic detachment and re‐colonization due to the regular changes in hydrodynamic forcing. However, legacy impacts of past microbial actions on current biofilm formation and the biostabilization of the substratum sands are yet to be fully understood. In this study, a systematic set of flume experiments were conducted to investigate the effects of different depositional histories. Changes in the erosion threshold and rate of erosion were determined from the time sequences of suspended sediment concentrations. The contents of extracellular polymeric substances (EPS) and particle morphology of the biofilm‐bound sandy matrix were analyzed. Surprisingly, biostabilization is disturbance‐stimulated, rather than disturbance‐limited, as previously thought. Bio‐sandy beds cultivated under intensive disturbance presented an EPS accumulation in each cycle, and showed a more rapid increase in bed strength and stability than when rarely disturbed. All colonies from previous cycles exhibited traces of EPS as “footprints”. These stimulated and possibly accelerated the process of recolonization, thereby enhancing the erosion resistance of the bed. In contrast, a stabilized bed was better suited to mature microbial communities. A modified “Windows of Opportunity” framework was therefore put forward. Although biostabilization was not established within short quiescent periods, the system created the “opportunity” to become established in subsequent “windows” by seeding the colonization process. The stabilization, destabilization and re‐stabilization of biofilm may imply a much more important role as ecosystem engineers and is relevant for a range of engineered bio‐systems.

Benthic Biofilm Bacterial Communities and Their Linkage with Water-Soluble Organic Matter in Effluent Receivers.

Benthic biofilms are pioneering microbial aggregates responding to effluent discharge from wastewater treatment plants (WWTPs). However, knowledge of the characteristics and linkage of bacterial communities and water-soluble organic matter (WSOM) of benthic biofilms in effluent-receiving rivers remains unknown. Here, we investigated the quality of WSOM and the evolution of bacterial communities in benthic biofilm to evaluate the ecological impacts of effluent discharge on a representative receiving water. Tryptophan-like proteins showed an increased proportion in biofilms collected from the discharge area and downstream from the WWTP, especially in summer. Biofilm WSOM showed weak humic character and strong autochthonous components, and species turnover was proven to be the main factor governing biofilm bacteria community diversity patterns. The bacterial community alpha diversity, interspecies interaction, biological index, and humification index were signally altered in the biofilms from the discharge area, while the values were more similar in biofilms collected upstream and downstream from the WWTP, indicating that both biofilm bacterial communities and WSOM characters have resilience capacities. Although effluent discharge simplified the network pattern of the biofilm bacterial community, its metabolic functional abundance was basically stable. The functional abundance of carbohydrate metabolism and amino acid metabolism in the discharge area increased, and the key modules in the non-random co-occurrence network also verified the important ecological role of carbon metabolism in the effluent-receiving river. The study sheds light on how benthic biofilms respond to effluent discharge from both ecological and material points of view, providing new insights on the feasibility of utilizing benthic biofilms as robust indicators reflecting river ecological health.

Benthic Biofilm Potential for Organic Carbon Accumulation in Salt Marsh Sediments

Coastal salt marshes are productive environments with high potential for carbon accumulation and storage. Even though organic carbon in salt marsh sediment is typically attributed to plant biomass, it can also be produced by benthic photosynthetic biofilms. These biofilms, generally composed of diatoms and their secretions, are known for their high primary productivity and contribution to the basal food web. The growth of biofilms and the preservation of carbon produced by biofilms depends on the amount of sedimentation; low sedimentation rates will favor decomposition, while high sedimentation rates could decrease biofilm productivity. In this study, we conducted laboratory experiments to test (1) if biofilms can potentially accumulate carbon in marsh soil and (2) how different sedimentation rates affect the amount of carbon accumulation. Containers filled with a settled mud bed were inoculated with natural biofilms collected from a marsh surface and allowed to grow with favorable light exposure, nutrient supply, and absence of grazing. Mud was added weekly in different amounts, resulting in an equivalent sedimentation rate from 12 to 189 mm/yr. After 11 weeks, the sediment columns were sampled and analyzed for chl a, organic matter via loss on ignition (LOI), and total organic carbon (TOC). Chl a accumulation rates ranged from 123 to 534 mg/cm2/yr, organic matter accumulation ranged from 86 to 456 g/m2/yr, and TOC accumulation rates ranged from 31 to 211 g/m2/yr. These values are on the same order of magnitude of marsh carbon accumulation rates measured in the field. All three metrics (chl a, organic matter, and TOC) increased with increased sedimentation rate. These results show that biofilms can potentially contribute to carbon accumulation in salt marsh soils. Furthermore, areas with high sedimentation rates have the potential for higher amounts of organic matter from biofilms in the sediment.

A workflow to investigate the impacts of weathered multi-walled carbon nanotubes to the mud snail Lymnaea stagnalis

Although the development and application of nanomaterials is a growing industry, little data is available on the ecotoxicological effects on aquatic organisms. Therefore, we set up a workflow to address the potential uptake of weathered multi-walled carbon nanotubes (wMWCNTs) by a model organism, the pulmonary mud snail Lymnaea stagnalis (L. stagnalis), which plays an important role in the food web. It represents a suitable organism for this approach because as a grazer it potentially ingests large amounts of sedimented wMWCNTs. As food source for L. stagnalis, benthic biofilm was investigated by the use of a transmission electron microscope (TEM) and a scanning electron microscope (SEM) after exposure with wMWCNTs. In addition, isotopic labeling was applied with 14C-wMWCNTs (0.1 mg/L) to quantify fate, behavior, and enrichment of 14C-wMWCNTs in benthic biofilm and in L. stagnalis. Enrichment in benthic biofilm amounted to 529.0 µg wMWCNTs/g dry weight and in L. stagnalis to 79.6 µg wMWCNTs/g dry weight. A bioconcentration factor (BCF) for L. stagnalis was calculated (3500 L/kg). We demonstrate the accumulation of wMWCNTs (10 mg/L) in the digestive tract of L. stagnalis in an effect study. Moreover, the physiological markers glycogen and triglycerides as indicators for the physiological state, as well as the RNA/DNA ratio as growth indicator, were examined. No significant differences between exposed and control animals were analyzed for glycogen and triglycerides after 24 days of exposure, but a decreasing trend is recognizable for triglycerides. In contrast, the significant reduction in the RNA/DNA ratio of L. stagnalis indicated an inhibition of growth with a following recovery after depuration. The described workflow enables a comprehensive determination of the fate and the behavior of wMWCNTs specifically and in general all kinds of CNTs in the aquatic environment and therefore contributes to a holistic risk assessment of wMWCNTs.

Easily Implemented Methods of Radiometric Corrections for Hyperspectral–UAV—Application to Guianese Equatorial Mudbanks Colonized by Pioneer Mangroves

Hyper-DRELIO (Hyperspectral DRone for Environmental and LIttoral Observations) is a custom, mini-UAV (unmanned aerial vehicle) platform (<20 kg), equipped with a light push broom hyperspectral sensor combined with a navigation module measuring position and orientation. Because of the particularities of UAV surveys (low flight altitude, small spatial scale, and high resolution), dedicated pre-processing methods have to be developed when reconstructing hyperspectral imagery. This article presents light, easy-implementation, in situ methods, using only two Spectralon® and a field spectrometer, allowing performance of an initial calibration of the sensor in order to correct “vignetting effects” and a field standardization to convert digital numbers (DN) collected by the hyperspectral camera to reflectance, taking into account the time-varying illumination conditions. Radiometric corrections are applied to a subset of a dataset collected above mudflats colonized by pioneer mangroves in French Guiana. The efficiency of the radiometric corrections is assessed by comparing spectra from Hyper-DRELIO imagery to in situ spectrometer measurements above the intertidal benthic biofilm and mangroves. The shapes of the spectra were consistent, and the spectral angle mapper (SAM) distance was 0.039 above the benthic biofilm and 0.159 above the mangroves. These preliminary results provide new perspectives for quantifying and mapping the benthic biofilm and mangroves at the scale of the Guianese intertidal mudbanks system, given their importance in the coastal food webs, biogeochemical cycles, and the sediment stabilization.

Digestion and assimilation of benthic biofilm by the Sábalo, Prochilodus lineatus.

The Sábalo, Prochilodus lineatus (Valenciennes, 1837), is one of 270 fish species in the Rio Paraná system, and it comprises >50% of the fish biomass. Its diet is flocculant benthic biofilm comprised of algae, bacteria and non-living organic matter: a food resource apparently of little value to other fishes. Digestion and assimilation of key nutrients from its biofilm diet by P. lineatus were described and quantified in an attempt to discover how this species is so successful. The fish begin a feeding period with empty digestive tracts, accumulate food during the feeding period and then void the gut content at the end of the feeding period. Early in a feeding period, sand accumulates in the gizzard-like pyloric stomach where it serves as both a grinding medium and a sieve. After sufficient sand has been acquired, food particles passed from the pyloric stomach to the intestine are dramatically reduced in size to <20 μ maximum dimension, whereas larger particles including mineral matter and plant fibres are retained. Total ash, hydrolysis-resistant-ash and hydrolysis-resistant-organic-matter were tested as reference materials against which to measure assimilation and hydrolysis-resistant-organic matter best met the assumptions of the technique. Comparison of the first food ingested to food ingested later in the feeding period shows that grinding of food and selective retention of larger particles results in a three-fold increase in the assimilation of ash-free-dry-mass (to 56%) and hydrolysis-labile-organic-matter (to 67%), and a six-fold increase in the assimilation of amino acids (AAs; to 74%). When food quality is assessed in terms of g AA assimilated · kJ-1 energy assimilated, the quality of food ingested by P. lineatus ranges from a maintenance level of 5 to 12 mg AA · kJ-1 , a level expected to produce near maximum growth. Thus, the processing of food in the pyloric stomach is integral to the success of P. lineatus in establishing large populations on a diet of flocculent benthic biofilm.

Physico-chemistry and adhesion kinetics of algal biofilm on polyethersulfone (PES) membrane with different surface wettability

Microalgal biofilm growth on porous substrates has recently garnered extensive attention with the advantage of high biomass productivity with low liquid culture volume. In such cultivation, the surface characteristics of supporting materials play essential role supporting biofilm growth. In view of this, a study on the membrane surface wettability of a commercial polyethersulfone (PES) membrane with two different hydrophilicities was selected in a long-term benthic biofilm cultivation experiment. Findings revealed that both soluble and bounded extracellular polymeric substances (EPS) contributed towards the formation of an adhesive gel layer onto the membrane’s surfaces. The maximum accumulated cell density was achieved by C. fusiformis around 47.64 ± 4.03 × 109 cells m−2 onto phobic PES (79.29°) and the least by N. incerta around 6.40 ± 0.49 × 109 cells m−2 onto philic PES (47.56°). The fact remained that the cell attachment rate was almost similar for both A. coffeaeformis and N. incerta but with gradual reduction after day 12 for phobic PES and day 8 for philic PES for the three benthic species. The change of adhesion ratio was well explained with their respective EPS variation. The XDLVO model employed suggested the dominance of acid-base interactions in high ionic strength liquid, leading to higher global minimum energy occurring on phobic PES. Overall, the findings indicated that biofilm formation is favored on polymer substrate having lower surface energy due to the attractive interaction of the submerged surface with those biomolecules and colloids.

Sediment underneath charophyte meadows is enriched in viable ephippia and enhances the benthic periphytic biofilm

We contribute to the knowledge of charophyte meadows as key components of aquatic systems by analysing how they affect wetland sediments. We performed a factorial-design experiment with limnocorrals (outdoor mesocosms) in a Mediterranean protected wetland with presence or absence of charophytes [Chara vulgaris (CV) and Chara hispida (CH), planted from cultures or recruited in situ from germination of their fructifications]. The first 1 cm-surficial and 2 cm-bottom sediment layers were analysed for cladoceran ephippia, ostracods valves, benthic community of bacteria and periphytic biofilm, and charophyte fructifications. In the surficial sediment, the ephippia density was fourfold higher in the conditions with charophytes than in sites with no-charophytes and higher apparent viability was found. The surficial sediment periphyton biofilm was composed mainly of diatoms, with tenfold higher biomass underneath charophytes, and a much diverse community. The specific microhabitat generated by each charophyte species was reflected in the different abundances and relationships between the analysed components, firstly establishing a divergence with the sediment without meadows and, secondly, a distinction between the meadows of CH and CV that exhibit particular morphology-architecture, might exudate different metabolites and might have different allelopathic capacities over microalgae and microinvertebrates. Thus, the charophyte–sediment tandem is relevant for biodiversity and habitat conservation.

Microbial biofilm community dynamics in five lowland streams

Stream biofilms are complex aggregates of diverse organism groups that play a vital role in global carbon and nitrogen cycles. Most of the current studies on stream biofilm focus on a limited number of organism groups (e.g., bacteria and algae), and few have included both prokaryote and eukaryote communities simultaneously. In this study, we incubated artificial substrates in five Danish lowland streams exhibiting different hydrological and physico-chemical conditions and explored the dynamics of community composition and diversity of the benthic biofilm, including both prokaryotes and eukaryotes. We found that few phyla in the prokaryote (Gammaproteobacteria and Bacteroidetes) and eukaryote (Cercozoa) communities accounted for over two-thirds of the total abundance at most of the sites. Both prokaryotic and eukaryotic diversity displayed the same temporal patterns, i.e., diversity peaked in July and January. We also found that hydrological and physico-chemical variables significantly explained the variation in the community composition at phylum level for both prokaryotes and eukaryotes. However, a large proportion of variation remained unexplained, which can be ascribed to important but unmeasured variables like light intensity and biological factors such as trophic and non-trophic interactions as revealed by network analysis. Therefore, we suggest that use of a multitrophic level perspective is needed to study biofilm i.e., the “microbial jungles”, where high occurrences of trophic and non-trophic interactions are expected.

Biofilm pigments in temporary streams indicate duration and severity of drying

AbstractIncreased duration and frequency of droughts under global change may affect both temporary and formerly permanent watercourses. Streambed desiccation, cooccurring solar radiation, and high temperature all may affect the composition and metabolism of photoautotrophic organisms in benthic biofilms. To test these effects, we characterized the composition of pigments when biofilms were exposed to dry conditions, and compared this to pigments measured after flow resumed, as well as to others measured from permanent streams in the same region. This comparison revealed important differences in pigmentary composition based on flow conditions. Active chlorophylls decreased exponentially with the duration and severity of the nonflow period, while chlorophyll degradation products and protective carotenoids increased. Streams experiencing longer and more severe nonflow periods showed the highest dissimilarities in their biofilm pigmentary composition, and this pattern was maintained after flow resumed. Our results pointed to duration of nonflowing periods as the major driver of pigmentary composition, regardless of whether these were interrupted or not by short intervals of water flows. Multivariate changes in pigmentary composition between sampling periods highlighted the influence of the long‐term hydrological history on the relative abundance of different taxonomic groups and their associated pigments. Overall, pigmentary fingerprints are informative of the biofilm capacity to resist water flow interruption and of their ability to recover after water flow returns.

Wildfire-Derived Pyrogenic Carbon Modulates Riverine Organic Matter and Biofilm Enzyme Activities in an In Situ Flume Experiment.

Wildfires produce large amounts of pyrogenic carbon (PyC), including charcoal, known for its chemical recalcitrance and sorption affinity for organic molecules. Wildfire-derived PyC can be transported to fluvial networks. Here it may alter the dissolved organic matter (DOM) concentration and composition as well as microbial biofilm functioning. Effects of PyC on carbon cycling in freshwater ecosystems remain poorly investigated. Employing in-stream flumes with a control versus treatment design (PyC pulse addition), we present evidence that field-aged PyC inputs to rivers can increase the dissolved organic carbon (DOC) concentration and alter the DOM composition. DOM fluorescence components were not affected by PyC. The in-stream DOM composition was altered due to leaching of pyrogenic DOM from PyC and possibly concurrent sorption of riverine DOM to PyC. Decreased DOM aromaticity indicated by a lower SUVA245 (−0.31 unit) and a higher pH (0.25 unit) was associated with changes in enzymatic activities in benthic biofilms, including a lower recalcitrance index (β-glucosidase/phenol oxidase), suggesting preferential usage of recalcitrant over readily available DOM by biofilms. The deposition of particulate PyC onto biofilms may further modulate the impacts of PyC due to direct contact with the biofilm matrix. This study highlights the importance of PyC for in-stream biogeochemical organic matter cycling in fire-affected watersheds.

Settlement and culture of post-larvae, spat and juveniles of the West Indian topshell, Cittarium pica (Linne, 1758)

The settlement, survival and growth rates of C. pica post-larvae, spat and juveniles were evaluated under different culture conditions. The factorial effect of six stimuli (low temperature, γ-aminobutyric acid, potassium chloride, hydrogen peroxide, dibromo methane, and coralline algae extract), five types of biofilm substrates (artificial, artificial with coralline algae, artificial with congener mucus, benthic microalgae, and microalgae with congeners mucus) and five stimulation times (6, 12, 24, 36 and 72 h) on the larval settlement of the topshell were assessed. In addition, growth and survival rates of post-larvae fed with artificial biofilm and benthic microalgae were compared. Similarly, growth and survival rates were assessed in spat cultured in different environments (outdoor and indoor), and juveniles grown in concrete tanks with different finished of the inner walls (gray rough finish, and white smooth walls with epoxy paint). A higher larval settlement was observed in substrates with artificial biofilm exposed to cold water (20 °C) for 24 h. Treatments with the stimulus of KCl and dibromo methane had toxic effects on larvae. There were not differences in the shell length of the settled larvae between stimuli, substrata or exposition time. Post-larvae fed with artificial biofilm had survival and growth rates similar to those maintained with benthic microalgae biofilm. The spat that were cultured in outdoor conditions showed a higher growth rate than those kept indoor, but the survival was similar in both cases. Finally, juveniles grown in tanks with rough, gray concrete inner walls had higher growth and survival rates, compared to those held in tanks with smooth white finish. The improvements obtained in growth and survival of post-larvae, spat and juveniles of C. pica suggest that there is a great biological potential for its wild populations restocking and for its aquaculture in sea-based systems.

Active Microbiome Structure and Functional Analyses of Freshwater Benthic Biofilm Samples Influenced by RNA Extraction Methods.

Advances in high-throughput sequencing technologies have enabled extensive studies of freshwater biofilms and significant breakthroughs in biofilm meta-omics. To date, however, no standardized protocols have been developed for the effective isolation of RNA from freshwater benthic biofilms. In this study, we compared column-based kit RNA extraction with five RNAzol-based extractions, differentiated by various protocol modifications. The RNA products were then evaluated to determine their integrity, purity and yield and were subjected to meta-transcriptomic sequencing and analysis. Significant discrepancies in the relative abundance of active communities and structures of eukaryotic, bacterial, archaebacterial, and viral communities were observed as direct outcomes of the tested RNA extraction methods. The column isolation-based group was characterized by the highest relative abundance of Archaea and Eukaryota, while the organic isolation-based groups commonly had the highest relative abundances of Prokaryota (bacteria). Kit extraction methods provided the best outcomes in terms of high-quality RNA yield and integrity. However, these methods were deemed questionable for studies of active bacterial communities and may contribute a significant degree of bias to the interpretation of downstream meta-transcriptomic analyses.

Do Electrofishing Activities Disrupt Stream Biofilm Standing Stocks? An Assessment from Two Headwater Streams in Western Oregon

AbstractHumans affect ecosystems in many ways, and scientific field studies are no exception. If data collection disrupts environments or biota too much, it can lead to inaccurate conclusions in the study of interest or in subsequent studies. We evaluated whether stream electrofishing surveys could measurably disturb the benthic biofilms in two forested headwaters in western Oregon, USA. While the consequences of electrofishing to macroinvertebrates and fish have been assessed, to date no studies have quantified its influence on benthic biofilms. We observed declines in the standing stocks of accrued benthic chlorophyll a directly after electrofishing in both streams. After electrofishing, the standing biofilm stocks declined by an average of ~15% in Oak Creek, a small third‐order stream in the Oregon Coast Range Mountains, and by an average of ~34% in a third‐order section of Lookout Creek, which is located in the western Cascade Mountains of Oregon, USA. In returning to Oak Creek 2 weeks after electrofishing, the standing stocks had fully recovered to their prefishing levels. While the benthic biofilm standing stocks did decline in association with electrofishing, the effects were small when compared with those of disturbances from common flow events and when scaling to the whole stream system. In Oak Creek, the proportional biofilm standing stock decline from electrofishing activity was about 26% of what was observed following a moderate flow event (40% of bank‐full discharge), and about 15% of the decline in biofilm standing stocks following a complete bank‐full discharge event (140% of bank‐full discharge).

Soil microbial inoculation during flood events shapes headwater stream microbial communities and diversity

Flood events are now recognized as potentially important occasions for the transfer of soil microbes to stream ecosystems. Yet, little is known about these “dynamic pulses of microbial life” for stream bacterial community composition (BCC) and diversity. In this study, we explored the potential alteration of stream BCC by soil inoculation during high flow events in six pre-alpine first order streams and the larger Oberer Seebach. During 1 year, we compared variations of BCC in soil water, stream water and in benthic biofilms at different flow conditions (low to intermediate flows versus high flow). Bacterial diversity was lowest in biofilms, followed by soils and highest in headwater streams and the Oberer Seebach. In headwater streams, bacterial diversity was significantly higher during high flow, as compared to low flow (Shannon diversity: 7.6 versus 7.9 at low versus high flow, respectively, p < 0.001). Approximately 70% of the bacterial operational taxonomic units (OTUs) from streams and stream biofilms were the same as in soil water, while in the latter one third of the OTUs were specific to high flow conditions. These soil high-flow OTUs were also found in streams and biofilms at other times of the year. These results demonstrate the relevance of floods in generating short and reoccurring inoculation events for flowing waters. Moreover, they show that soil microbial inoculation during high flow enhances microbial diversity and shapes fluvial BCC even during low flow. Hence, soil microbial inoculation during floods could act as a previously overlooked driver of microbial diversity in headwater streams.

Long-term impacts of nutrient control, climate change, and invasive clams on phytoplankton and cyanobacteria biomass in a large temperate river

Recent studies suggest that climate change, with warmer water temperatures and lower and longer low flows, may enhance harmful planktic cyanobacterial growth in lakes and large rivers. Concomitantly, controlling nutrient loadings has proven effective in reducing phytoplankton biomass especially in North America and Western Europe. In addition, the impact of invasive benthic filter-feeder species such as Corbicula on phytoplankton has largely been overlooked in large rivers, leading to even more uncertainty in predicting future trajectories in river water quality.To investigate how nutrient control, climate change and invasion of benthic filter-feeders may affect phytoplankton biomass and composition, we assembled a large database on the entire water course of the River Loire (France) over three decades (1991–2019). We focus on cyanobacteria to provide an in-depth analysis of the 30-year trend and insights on future possible trajectories. Since 1991, total phytoplankton and cyanobacteria biomasses have decreased 10-fold despite warmer water temperature (+0.23 °C·decade−1) and lower summer flow (−0.25 L·s−1·km−2·decade−1). In the long-term, the contribution of planktic cyanobacteria to total biomass was on average 2.8%. The main factors driving total phytoplankton and cyanobacteria biomasses were total phosphorus (4-fold decrease), the abundance of Corbicula clams (from absence before 1998 to 250–1250 individuals·m−2 after 2010), the duration of summer low flows and the intensity of summer heatwaves. The River Loire constitutes an example in Europe of how nutrient control can be an efficient mitigation strategy, counteracting already visible effects of climate change on the thermal regime and flow pattern of the river. This may hold true under future conditions, but further work is needed to account for the climate trajectory, land and water use scenarios, the risk of enhanced benthic biofilm and macrophyte proliferation, together with the spread of invasive filter-feeding bivalves.

Patterns and Drivers of Extracellular Enzyme Activity in New Zealand Glacier-Fed Streams.

Glacier-fed streams (GFSs) exhibit near-freezing temperatures, variable flows, and often high turbidities. Currently, the rapid shrinkage of mountain glaciers is altering the delivery of meltwater, solutes, and particulate matter to GFSs, with unknown consequences for their ecology. Benthic biofilms dominate microbial life in GFSs, and play a major role in their biogeochemical cycling. Mineralization is likely an important process for microbes to meet elemental budgets in these systems due to commonly oligotrophic conditions, and extracellular enzymes retained within the biofilm enable the degradation of organic matter and acquisition of carbon (C), nitrogen (N), and phosphorus (P). The measurement and comparison of these extracellular enzyme activities (EEA) can in turn provide insight into microbial elemental acquisition effort relative to environmental availability. To better understand how benthic biofilm communities meet resource demands, and how this might shift as glaciers vanish under climate change, we investigated biofilm EEA in 20 GFSs varying in glacier influence from New Zealand’s Southern Alps. Using turbidity and distance to the glacier snout normalized for glacier size as proxies for glacier influence, we found that bacterial abundance (BA), chlorophyll a (Chl a), extracellular polymeric substances (EPS), and total EEA per gram of sediment increased with decreasing glacier influence. Yet, when normalized by BA, EPS decreased with decreasing glacier influence, Chl a still increased, and there was no relationship with total EEA. Based on EEA ratios, we found that the majority of GFS microbial communities were N-limited, with a few streams of different underlying bedrock geology exhibiting P-limitation. Cell-specific C-acquiring EEA was positively related to the ratio of Chl a to BA, presumably reflecting the utilization of algal exudates. Meanwhile, cell-specific N-acquiring EEA were positively correlated with the concentration of dissolved inorganic nitrogen (DIN), and both N- and P-acquiring EEA increased with greater cell-specific EPS. Overall, our results reveal greater glacier influence to be negatively related to GFS biofilm biomass parameters, and generally associated with greater microbial N demand. These results help to illuminate the ecology of GFS biofilms, along with their biogeochemical response to a shifting habitat template with ongoing climate change.

Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams.

Glacier-fed streams (GFS) are harsh ecosystems dominated by microbial life organized in benthic biofilms, yet the biodiversity and ecosystem functions provided by these communities remain under-appreciated. To better understand the microbial processes and communities contributing to GFS ecosystems, it is necessary to leverage high throughput sequencing. Low biomass and high inorganic particle load in GFS sediment samples may affect nucleic acid extraction efficiency using extraction methods tailored to other extreme environments such as deep-sea sediments. Here, we benchmarked the utility and efficacy of four extraction protocols, including an up-scaled phenol-chloroform protocol. We found that established protocols for comparable sample types consistently failed to yield sufficient high-quality DNA, delineating the extreme character of GFS. The methods differed in the success of downstream applications such as library preparation and sequencing. An adapted phenol-chloroform-based extraction method resulted in higher yields and better recovered the expected taxonomic profile and abundance of reconstructed genomes when compared to commercially-available methods. Affordable and straight-forward, this method consistently recapitulated the abundance and genomes of a mock community, including eukaryotes. Moreover, by increasing the amount of input sediment, the protocol is readily adjustable to the microbial load of the processed samples without compromising protocol efficiency. Our study provides a first systematic and extensive analysis of the different options for extraction of nucleic acids from glacier-fed streams for high-throughput sequencing applications, which may be applied to other extreme environments.

Substratum-associated microbiota.

Highlights of new, interesting, and emerging research findings on substratum-associated microbiota covered from a survey of 2019 literature from primarily freshwaters provide insight into research trends of interest to the Water Environment Federation and others interested in benthic, aquatic environments. Coverage of topics on bottom-associated or attached algae and cyanobacteria, though not comprehensive, includes new methods, taxa new-to-science, nutrient dynamics, auto- and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, and bloom-forming and harmful algae. Coverage of bacteria, also not comprehensive, focuses on the ecology of benthic biofilms and microbial communities, along with the ecology of microbes like Caulobacter crescentus, Rhodobacter, and other freshwater microbial species. Bacterial topics covered also include metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Readers may use this literature review to learn about or renew their interest in the recent advances and discoveries regarding substratum-associated microbiota. PRACTITIONER POINTS: This review of literature from 2019 on substratum-associated microbiota presents highlights of findings on algae, cyanobacteria, and bacteria from primarily freshwaters. Coverage of algae and cyanobacteria includes findings on new methods, taxa new to science, nutrient dynamics, auto- and heterotrophic interactions, grazers, bioassessment, herbicides and other pollutants, metal contaminants, and nuisance, bloom-forming and harmful algae. Coverage of bacteria includes findings on ecology of benthic biofilms and microbial communities, the ecology of microbes, metagenomics and metatranscriptomics, toxins and pollutants, bacterial pathogens and bacteriophages, and bacterial physiology. Highlights of new, noteworthy and emerging topics build on those from 2018 and will be of relevance to the Water Environment Federation and others interested in benthic, aquatic environments.