Effects of bacterial inoculation and nitrogen loading on bacterial-algal consortium composition and functions in an integrated photobioelectrochemical system

An integrated photo-bioelectrochemical system (IPB) for wastewater treatment combines a microbial fuel cell with an algal bioreactor, eliminating requirements for aeration, promoting electricity generation, remediating nutrients and producing algal biomass for conversion into biofuel or other bioproducts. To examine strategies for improving IPB functions of electrochemical output and nutrient removal efficiency, this study tested effects of cathode bacterial inoculation and nitrogen loading on cathode microbial community and IPB performance. IPB cathodes were inoculated with the green alga Chlorella vulgaris, in combination with nitrite-oxidizing bacteria (NOB) Nitrobacter winogradskyi, and/or ammonium-oxidizing bacteria (AOB) Nitrosomonas europaea. IPB performance was examined before and after nitrifying bacteria inoculations and under three ammonium loading concentrations in the wastewater medium. Bacterial communities in the cathode suspension and biofilm were examined by 16S rRNA gene sequence analysis. Relative to the algae only control, cathode inoculation with NOB and/or AOB improved net nutrient removal, but resulted in reduced dissolved oxygen availability, which impaired electricity generation. Higher ammonium loading increased electricity production and nutrient removal, possibly by overcoming algal-bacterial competition. Inoculation with nitrifying bacteria resulted in minor changes to total bacterial composition and AOB or NOB comprised <3% of total sequences after 1 month. Community composition changed more dramatically following increase in ammonium-N concentration from 40 to 80 mg L^-1. Manipulation of N loading could be a useful strategy to improve IPB performance, while inoculation of AOB or NOB may be beneficial for treatment of water with high ammonium loading when N removal is the primary system goal.

Natural Communities of Carotenogenic Chlorophyte Haematococcus lacustris and Bacteria from the White Sea Coastal Rock Ponds

Haematococcus lacustris is a biotechnologically important green unicellular alga producing widely used keta-karotenoid astaxanthin. In natural habitats, it exists in the form of algal-bacterial community, and under laboratory conditions, it is also accompanied by bacteria. The issue of the bacterial composition of industrial algal cultures is widely recognized as important. However, there is a dearth of information about bacterial composition of H. lacustris communities. In current work, we analyze the composition of natural H. lacustris communities from the White Sea coastal temporal rock ponds. For the first time, a 16S rRNA gene-based metagenome of natural H. lacustris bacterial communities has been generated. Main results of its analysis are as follow. Bacterial families Comamonadaceae, Cytophagaceae, Xanthomonadaceae, Acetobacteraceae, Rhodobacteraceae, and Rhodocyclaceae were observed in all studied H. lacustris natural communities. They also contained genera Hydrogenophaga and Cytophaga. Bacteria from the Hydrogenophaga genus were present in H. lacustris cultures after their isolation under the conditions of laboratory cultivation. Similar to other planktonic microalgae, H. lacustris forms a phycosphere around the cells. In this zone, bacteria attached to the algal surface. The contact between H. lacustris and bacteria is maintained even after sample drying. The study provides information about possible members of H. lacustris core microbiome, which can be presented in the industrial and laboratory cultures of the microalga.

Activated carbon promotes short-chain fatty acids production from algae during anaerobic fermentation

Alkaline pH was beneficial for short-chain fatty acids (SCFAs) production from algae during anaerobic fermentation. This study focused on the effects of activated carbon on SCFAs production from algae during alkaline anaerobic fermentation. When activated carbon was present at 0.5 g/L, the maximum production of SCFAs was 4875 mg COD/L, which was nearly 2.4 times that of the control (2026 mg/L). Moreover, the fermentation time required for the highest SCFAs production was shortened from 6 d in the control to 4 d with activated carbon. Mechanism exploration revealed that solubilization and hydrolysis of algae as well as activities of key hydrolases and quantities of encoding genes were improved in the presence of activated carbon, which provided more proteins and carbohydrates for acid-forming bacteria. More importantly, the electron transfer among microorganisms in the algae fermentation systems was enhanced by activated carbon, contributing to improvement of the SCFAs yield and reduction of fermentation time.

Bioreactivity and Microbiome of Biodeposits from Filter-Feeding Bivalves

Bivalves serve an important ecosystem function in delivering organic matter from pelagic to benthic zones and are important in mediating eutrophication. However, the fate of this organic matter (i.e., biodeposits) is an important consideration when assessing the ecological roles of these organisms in coastal ecosystems. In addition to environmental conditions, the processing of biodeposits is dependent on its composition and the metabolic capacity of the associated microbial community. The objectives of this study were to compare the biological reactivity, potential denitrification rates, and microbial communities of biodeposits sourced from different bivalve species: hard clam (Mercenaria mercenaria), eastern oyster (Crassostrea virginica), and ribbed mussel (Geukensia demissa). To our knowledge, this is the first study to investigate and compare the microbiome of bivalve biodeposits using high-throughput sequencing and provide important insight into the mechanisms by which bivalves may alter sediment microbial communities and benthic biogeochemical cycles. We show that clam biodeposits had significantly higher bioreactivity compared to mussel and oyster biodeposits, as reflected in higher dissolved inorganic carbon and ammonium production rates in controlled incubations. Potential denitrification rates were also significantly higher for clam biodeposits compared to oyster and mussel biodeposits. The microbial communities associated with the biodeposits were significantly different across bivalve species, with significantly greater abundances of Alteromonadales, Chitinophagales, Rhodobacterales, and Thiotrichales associated with the clam biodeposits. These bioreactivity and microbial differences across bivalve species are likely due to differences in bivalve physiology and feeding behavior and should be considered when evaluating the effects of bivalves on water quality and ecosystem function.

Seaweed Loads Cause Stronger Bacterial Community Shifts in Coastal Lagoon Sediments Than Nutrient Loads

The input of nutrients from anthropogenic sources is the leading cause of coastal eutrophication and is usually coupled with algal/seaweed blooms. Effects may be magnified in semi-enclosed systems, such as highly productive coastal lagoon ecosystems. Eutrophication and seaweed blooms can lead to ecosystem disruption. Previous studies have considered only one of these factors, disregarding possible interactive effects and the effect of the blooming species' identity on sediment bacterial communities. We tested the effect of experimental nutrient loading and two common blooming seaweeds (Ulva rigida and Gracilaria vermiculophylla) in coastal lagoon sediments, on the structure of bacterial communities (using 16S rRNA amplicon sequencing) and corresponding putative functional potential (using PiCRUSt). At the Operational Taxonomic Unit (OTU) level, the addition of nutrients reduced bacterial community α-diversity and decreased the abundance of sulfate reducers (Desulfobacterales) compared to sulfur oxidizers/denitrifiers (Chromatiales and Campylobacterales), whereas this was not the case at the order level. Seaweed addition did not change bacterial α-diversity and the effect on community structure depended on the taxonomic level considered. The addition of Gracilaria increased the abundance of orders and OTUs involved in sulfate reduction and organic matter decomposition (Desulfobacterales, Bacteroidales, and Clostridiales, respectively), an effect which was also detected when only Ulva was added. Nutrients and the seaweeds combined only interacted for Ulva and nutrients, which increased known sulfide oxidizers and denitrifiers (order Campylobacterales). Seaweed enrichment affected putative functional profiles; a stronger increase of sulfur cycling KEGG pathways was assigned to nutrient-disturbed sediments, particularly with the seaweeds and especially Ulva. In contrast, nitrogen and sulfur cycle pathways showed a higher abundance of genes related to dissimilatory nitrate reduction to ammonium (DNRA) in Ulva+nutrients treatments. However, the other seaweed treatments increased the nitrogen fixation genes. Thiosulfate reduction, performed by sulfate-reducing bacteria, increased in seaweed treatments except when Ulva was combined with nutrients. In conclusion, the in situ addition of nutrients and the seaweeds to intertidal sediments affected the bacterial communities differently and independently. The predicted functional profile suggests a shift in relative abundances of putative pathways for nitrogen and sulfur cycles, in line with the taxonomic changes of the bacterial communities.

Genome-scale fitness profile of Caulobacter crescentus grown in natural freshwater

Bacterial genomes evolve in complex ecosystems and are best understood in this natural context, but replicating such conditions in the lab is challenging. We used transposon sequencing to define the fitness consequences of gene disruption in the bacterium Caulobacter crescentus grown in natural freshwater, compared with axenic growth in common laboratory media. Gene disruptions in amino-acid and nucleotide sugar biosynthesis pathways and in metabolic substrate transport machinery impaired fitness in both lake water and defined minimal medium relative to complex peptone broth. Fitness in lake water was enhanced by insertions in genes required for flagellum biosynthesis and reduced by insertions in genes involved in biosynthesis of the holdfast surface adhesin. We further uncovered numerous hypothetical and uncharacterized genes for which disruption impaired fitness in lake water, defined minimal medium, or both. At the genome scale, the fitness profile of mutants cultivated in lake water was more similar to that in complex peptone broth than in defined minimal medium. Microfiltration of lake water did not significantly affect the terminal cell density or the fitness profile of the transposon mutant pool, suggesting that Caulobacter does not strongly interact with other microbes in this ecosystem on the measured timescale. Fitness of select mutants with defects in cell surface biosynthesis and environmental sensing were significantly more variable across days in lake water than in defined medium, presumably owing to day-to-day heterogeneity in the lake environment. This study reveals genetic interactions between Caulobacter and a natural freshwater environment, and provides a new avenue to study gene function in complex ecosystems.

Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment

Targeted qPCR and non-targeted amplicon sequencing of 16S rRNA genes within sediment layers identified the anaerobic ammonium oxidation (anammox) niche and characterized microbial community changes attributable to freshwater mussels. Anammox bacteria were normally distributed (Shapiro-Wilk normality test, W-statistic =0.954, p = 0.773) between 1 and 15 cm depth and were increased by a factor of 2.2 (p < 0.001) at 3 cm below the water-sediment interface when mussels were present. Amplicon sequencing of sediment at depths relevant to mussel burrowing (3 and 5 cm) showed that mussel presence reduced observed species richness (p = 0.005), Chao1 diversity (p = 0.005), and Shannon diversity (p < 0.001), with more pronounced decreases at 5 cm depth. A non-metric, multidimensional scaling model showed that intersample microbial species diversity varied as a function of mussel presence, indicating that sediment below mussels harbored distinct microbial communities. Mussel presence corresponded with a 4-fold decrease in a majority of operational taxonomic units (OTUs) classified in the phyla Gemmatimonadetes, Actinobacteria, Acidobacteria, Plantomycetes, Chloroflexi, Firmicutes, Crenarcheota, and Verrucomicrobia. 38 OTUs in the phylum Nitrospirae were differentially abundant (p < 0.001) with mussels, resulting in an overall increase from 25% to 35%. Nitrogen (N)-cycle OTUs significantly impacted by mussels belonged to anammmox genus Candidatus Brocadia, ammonium oxidizing bacteria family Nitrosomonadaceae, ammonium oxidizing archaea genus Candidatus Nitrososphaera, nitrite oxidizing bacteria in genus Nitrospira, and nitrate- and nitrite-dependent anaerobic methane oxidizing organisms in the archaeal family “ANME-2d” and bacterial phylum “NC10”, respectively. Nitrosomonadaceae (0.9-fold (p < 0.001)) increased with mussels, while NC10 (2.1-fold (p < 0.001)), ANME-2d (1.8-fold (p < 0.001)), and Candidatus Nitrososphaera (1.5-fold (p < 0.001)) decreased with mussels. Co-occurrence of 2-fold increases in Candidatus Brocadia and Nitrospira in shallow sediments suggests that mussels may enhance microbial niches at the interface of oxic–anoxic conditions, presumably through biodeposition and burrowing. Furthermore, it is likely that the niches of Candidatus Nitrososphaera and nitrite- and nitrate-dependent anaerobic methane oxidizers were suppressed by mussel biodeposition and sediment aeration, as these phylotypes require low ammonium concentrations and anoxic conditions, respectively. As far as we know, this is the first study to characterize freshwater mussel impacts on microbial diversity and the vertical distribution of N-cycle microorganisms in upper Mississippi river sediment. These findings advance our understanding of ecosystem services provided by mussels and their impact on aquatic biogeochemical N-cycling.

Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder

Freshwater bacteria play fundamental roles in global elemental cycling and are an intrinsic part of local food webs. Human activities are altering freshwater environments, and much has been learned regarding the sensitivity of bacterial assemblages to a variety of these disturbances. Yet, relatively few studies have focused on how species invasion, which is one of the most important aspects of anthropogenic global change, affects freshwater bacterial assemblages. This study focuses on the impact of invasive dreissenid mussels (IDMs), a globally distributed group of invasive species with large impacts on freshwater phyto- and zooplankton assemblages. We show that IDMs have direct effects on lake bacterioplankton abundance, taxonomic composition, and inferred bacterial functional group representation.

One approach to improve forecasts of how global change will affect ecosystem processes is to better understand how anthropogenic disturbances alter bacterial assemblages that drive biogeochemical cycles. Species invasions are important contributors to global change, but their impacts on bacterial community ecology are rarely investigated. Here, we studied direct impacts of invasive dreissenid mussels (IDMs), one of many invasive filter feeders, on freshwater lake bacterioplankton. We demonstrated that direct effects of IDMs reduced bacterial abundance and altered assemblage composition by preferentially removing larger and particle-associated bacteria. While this increased the relative abundances of many free-living bacterial taxa, some were susceptible to filter feeding, in line with efficient removal of phytoplankton cells of <2 μm. This selective removal of particle-associated and larger bacteria by IDMs altered inferred bacterial functional group representation, defined by carbon and energy source utilization. Specifically, we inferred an increased relative abundance of chemoorganoheterotrophs predicted to be capable of rhodopsin-dependent energy generation. In contrast to the few previous studies that have focused on the longer-term combined direct and indirect effects of IDMs on bacterioplankton, our study showed that IDMs act directly as a biological disturbance to which freshwater bacterial assemblages are sensitive. The negative impacts on particle-associated bacteria, which have been shown to be more active than free-living bacteria, and the inferred shifts in functional group representation raise the possibility that IDMs may directly alter bacterially mediated ecosystem functions.

IMPORTANCE Freshwater bacteria play fundamental roles in global elemental cycling and are an intrinsic part of local food webs. Human activities are altering freshwater environments, and much has been learned regarding the sensitivity of bacterial assemblages to a variety of these disturbances. Yet, relatively few studies have focused on how species invasion, which is one of the most important aspects of anthropogenic global change, affects freshwater bacterial assemblages. This study focuses on the impact of invasive dreissenid mussels (IDMs), a globally distributed group of invasive species with large impacts on freshwater phyto- and zooplankton assemblages. We show that IDMs have direct effects on lake bacterioplankton abundance, taxonomic composition, and inferred bacterial functional group representation.

Influence of Land Use, Nutrients, and Geography on Microbial Communities and Fecal Indicator Abundance at Lake Michigan Beaches

Microbial communities within beach sand play a key role in nutrient cycling and are important to the nearshore ecosystem function. Escherichia coli and enterococci, two common indicators of fecal pollution, have been shown to persist in the beach sand, but little is known about how microbial community assemblages are related to these fecal indicator bacteria (FIB) reservoirs. We examined eight beaches across a geographic gradient and range of land use types and characterized the indigenous community structure in the water and the backshore, berm, and submerged sands. FIB were found at similar levels in sand at beaches adjacent to urban, forested, and agricultural land and in both the berm and backshore. However, there were striking differences in the berm and backshore microbial communities, even within the same beach, reflecting the very different environmental conditions in these beach zones in which FIB can survive. In contrast, the microbial communities in a particular beach zone were similar among beaches, including at beaches on opposite shores of Lake Michigan. The differences in the microbial communities that did exist within a beach zone correlated to nutrient levels, which varied among geographic locations. Total organic carbon and total phosphorus were higher in Wisconsin beach sand than in beach sand from Michigan. Within predominate genera, fine-scale sequence differences could be found that distinguished the populations from the two states, suggesting a biogeographic effect. This work demonstrates that microbial communities are reflective of environmental conditions at freshwater beaches and are able to provide useful information regarding long-term anthropogenic stress.