Fate of heterotrophic bacteria in Lake Tanganyika (East Africa)

The Effect of Protozoa Indigenous to Lakewater and Wastewater on Decay of Fecal Indicator Bacteria and Coliphage

Fecal indicator bacteria (FIB: Escherichia coli and enterococci) are used to assess recreational water quality. Viral indicators (i.e., somatic and F+ coliphage), could improve the prediction of viral pathogens in recreational waters, however, the impact of environmental factors, including the effect of predatory protozoa source, on their survival in water is poorly understood. We investigated the effect of lakewater or wastewater protozoa, on the decay (decreasing concentrations over time) of culturable FIB and coliphages under sunlight and shaded conditions. FIB decay was generally greater than the coliphages and was more rapid when indicators were exposed to lake vs. wastewater protozoa. F+ coliphage decay was the least affected by experimental variables. Somatic coliphage decayed fastest in the presence of wastewater protozoa and sunlight, though their decay under shaded conditions was-10-fold less than F+ after 14 days. The protozoa source consistently contributed significantly to the decay of FIB, and somatic, though not the F+ coliphage. Sunlight generally accelerated decay, and shade reduced somatic coliphage decay to the lowest level among all the indicators. Differential responses of FIB, somatic, and F+ coliphages to environmental factors support the need for studies that address the relationship between the decay of coliphages and viral pathogens under environmentally relevant conditions.

Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika

Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth's surface. LT's mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT's 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted to bring increased stratification and anoxia to freshwater lakes.

Decay of infectious adenovirus and coliphages in freshwater habitats is differentially affected by ambient sunlight and the presence of indigenous protozoa communities

BACKGROUND

Sanitary quality of recreational waters worldwide is assessed using fecal indicator bacteria (FIB), such as Escherichia coli and enterococci. However, fate and transport characteristics of FIB in aquatic habitats can differ from those of viral pathogens which have been identified as main etiologic agents of recreational waterborne illness. Coliphages (bacteriophages infecting E. coli) are an attractive alternative to FIB because of their many morphological and structural similarities to viral pathogens.

METHODS

In this in situ field study, we used a submersible aquatic mesocosm to compare decay characteristics of somatic and F+ coliphages to those of infectious human adenovirus 2 in a freshwater lake. In addition, we also evaluated the effect of ambient sunlight (and associated UV irradiation) and indigenous protozoan communities on decay of somatic and F+ coliphage, as well as infectious adenovirus.

RESULTS

Our results show that decay of coliphages and adenovirus was similar (p = 0.0794), indicating that both of these bacteriophage groups are adequate surrogates for decay of human adenoviruses. Overall, after 8 days the greatest log10 reductions were observed when viruses were exposed to a combination of biotic and abiotic factors (2.92 ± 0.39, 4.48 ± 0.38, 3.40 ± 0.19 for somatic coliphages, F+ coliphages and adenovirus, respectively). Both, indigenous protozoa and ambient sunlight, were important contributors to decay of all three viruses, although the magnitude of that effect differed over time and across viral targets.

CONCLUSIONS

While all viruses studied decayed significantly faster (p < 0.0001) when exposed to ambient sunlight, somatic coliphages were particularly susceptible to sunlight irradiation suggesting a potentially different mechanism of UV damage compared to F+ coliphages and adenoviruses. Presence of indigenous protozoan communities was also a significant contributor (p value range: 0.0016 to < 0.0001) to decay of coliphages and adenovirus suggesting that this rarely studied biotic factor is an important driver of viral reductions in freshwater aquatic habitats.

Persistence and Decay of Fecal Microbiota in Aquatic Habitats

Fecal microorganisms can enter water bodies in diverse ways, including runoff, sewage discharge, and direct fecal deposition. Once in water, the microorganisms experience conditions that are very different from intestinal habitats. The transition from host to aquatic environment may lead to rapid inactivation, some degree of persistence, or growth. Microorganisms may remain planktonic, be deposited in sediment, wash up on beaches, or attach to aquatic vegetation. Each of these habitats offers a panoply of different stressors or advantages, including UV light exposure, temperature fluctuations, salinity, nutrient availability, and biotic interactions with the indigenous microbiota (e.g., predation and/or competition). The host sources of fecal microorganisms are likewise numerous, including wildlife, pets, livestock, and humans. Most of these microorganisms are unlikely to affect human health, but certain taxa can cause waterborne disease. Others signal increased probability of pathogen presence, e.g., the fecal indicator bacteria Escherichia coli and enterococci and bacteriophages, or act as fecal source identifiers (microbial source tracking markers). The effects of environmental factors on decay are frequently inconsistent across microbial species, fecal sources, and measurement strategies (e.g., culture versus molecular). Therefore, broad generalizations about the fate of fecal microorganisms in aquatic environments are problematic, compromising efforts to predict microbial decay and health risk from contamination events. This review summarizes the recent literature on decay of fecal microorganisms in aquatic environments, recognizes defensible generalizations, and identifies knowledge gaps that may provide particularly fruitful avenues for obtaining a better understanding of the fates of these organisms in aquatic environments.

Microbial Food-Web Drivers in Tropical Reservoirs

Element cycling in aquatic systems is driven chiefly by planktonic processes, and the structure of the planktonic food web determines the efficiency of carbon transfer through trophic levels. However, few studies have comprehensively evaluated all planktonic food-web components in tropical regions. The aim of this study was to unravel the top-down controls (metazooplankton community structure), bottom-up controls (resource availability), and hydrologic (water residence time) and physical (temperature) variables that affect different components of the microbial food web (MFW) carbon stock in tropical reservoirs, through structural equation models (SEM). We conducted a field study in four deep Brazilian reservoirs (Balbina, Tucuruí, Três Marias, and Funil) with different trophic states (oligo-, meso-, and eutrophic). We found evidence of a high contribution of the MFW (up to 50% of total planktonic carbon), especially in the less-eutrophic reservoirs (Balbina and Tucuruí). Bottom-up and top-down effects assessed through SEM indicated negative interactions between soluble reactive phosphorus and phototrophic picoplankton (PPP), dissolved inorganic nitrogen, and heterotrophic nanoflagellates (HNF). Copepods positively affected ciliates, and cladocerans positively affected heterotrophic bacteria (HB) and PPP. Higher copepod/cladoceran ratios and an indirect positive effect of copepods on HB might strengthen HB-HNF coupling. We also found low values for the degree of uncoupling (D) and a low HNF/HB ratio compared with literature data (mostly from temperate regions). This study demonstrates the importance of evaluating the whole size spectrum (including microbial compartments) of the different planktonic compartments, in order to capture the complex carbon dynamics of tropical aquatic ecosystems.

Coupling Between Heterotrophic Nanoflagellates and Bacteria in Fresh Waters: Does Latitude Make a Difference?

Recent studies reported comparatively lower heterotrophic bacteria (HB) abundances in tropical regions, indicating that factors involved in bacterial losses could be more relevant in the tropics. Heterotrophic nanoflagellates (HNF) are considered the main predators of HB in aquatic ecosystems, and one should expect higher abundances in the tropics because of differences in the food web configuration (absence of large daphnids). However, there are no comprehensive studies comparing HB and HNF abundances in a latitudinal gradient. We hypothesized that HB abundance would be lower in the tropics because HNF abundance would be higher, resulting in a tighter HNF–HB coupling. To test this hypothesis, we compiled a large dataset of HB and HNF abundances from tropical and temperate freshwater environments. We found that both HB and HNF abundances were lower in the tropical region, and that HNF-HB coupling does not differ between temperate and tropical regions. The lower HNF abundance and lack of coupling may be explained by a strong top-down control on HNF and/or their herbivory preference. Besides, no relationship was found between bacterial specific growth rate and either chlorophyll-a and HB abundance, indicating that bacterial losses may have an important role in tropical freshwaters. Thus, we found that HNF is likely not the main controllers of HB abundance, and that grazing by ciliates and cladocerans, together with the physiological effects of higher temperatures, may explain the high bacterial loss rates in the tropics.

A New Comparative-Genomics Approach for Defining Phenotype-Specific Indicators Reveals Specific Genetic Markers in Predatory Bacteria

Predatory bacteria seek and consume other live bacteria. Although belonging to taxonomically diverse groups, relatively few bacterial predator species are known. Consequently, it is difficult to assess the impact of predation within the bacterial realm. As no genetic signatures distinguishing them from non-predatory bacteria are known, genomic resources cannot be exploited to uncover novel predators. In order to identify genes specific to predatory bacteria, we developed a bioinformatic tool called DiffGene. This tool automatically identifies marker genes that are specific to phenotypic or taxonomic groups, by mapping the complete gene content of all available fully-sequenced genomes for the presence/absence of each gene in each genome. A putative ‘predator region’ of ~60 amino acids in the tryptophan 2,3-dioxygenase (TDO) protein was found to probably be a predator-specific marker. This region is found in all known obligate predator and a few facultative predator genomes, and is absent from most facultative predators and all non-predatory bacteria. We designed PCR primers that uniquely amplify a ~180bp-long sequence within the predators’ TDO gene, and validated them in monocultures as well as in metagenetic analysis of environmental wastewater samples. This marker, in addition to its usage in predator identification and phylogenetics, may finally permit reliable enumeration and cataloguing of predatory bacteria from environmental samples, as well as uncovering novel predators.

Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water

Microbial decay processes are one of the mechanisms whereby sewage contamination is reduced in the environment. This decomposition process involves a highly complex array of bacterial and eukaryotic communities from both sewage and ambient waters. However, relatively little is known about how these communities change due to mixing and subsequent decomposition of the sewage contaminant. We investigated decay of sewage in upper Mississippi River using Illumina sequencing of 16S and 18S rRNA gene hypervariable regions and qPCR for human-associated and general fecal Bacteroidales indicators. Mixtures of primary treated sewage and river water were placed in dialysis bags and incubated in situ under ambient conditions for seven days. We assessed changes in microbial community composition under two treatments in a replicated factorial design: sunlight exposure versus shaded and presence versus absence of native river microbiota. Initial diversity was higher in sewage compared to river water for 16S sequences, but the reverse was observed for 18S sequences. Both treatments significantly shifted community composition for eukaryotes and bacteria (P < 0.05). Data indicated that the presence of native river microbiota, rather than exposure to sunlight, accounted for the majority of variation between treatments for both 16S (R = 0.50; P > 0.001) and 18S (R = 0.91; P = 0.001) communities. A comparison of 16S sequence data and fecal indicator qPCR measurements indicated that the latter was a good predictor of overall bacterial community change over time (rho: 0.804-0.814, P = 0.001). These findings suggest that biotic interactions, such as predation by bacterivorous protozoa, can be critical factors in the decomposition of sewage in freshwater habitats and support the use of Bacteroidales genetic markers as indicators of fecal pollution.

Abundance, diversity and seasonal dynamics of predatory bacteria in aquaculture zero discharge systems

Standard aquaculture generates large-scale pollution and strains water resources. In aquaculture using zero discharge systems (ZDS), highly efficient fish growth and water recycling are combined. The wastewater stream is directed through compartments in which beneficial microbial activities induced by creating suitable environmental conditions remove biological and chemical pollutants, alleviating both problems. Bacterial predators, preying on bacterial populations in the ZDS, may affect their diversity, composition and functional redundancy, yet in-depth understanding of this phenomenon is lacking. The dynamics of populations belonging to the obligate predators Bdellovibrio and like organisms (BALOs) were analyzed in freshwater and saline ZDS over a 7-month period using QPCR targeting the Bdellovibrionaceae, and the Bacteriovorax and Bacteriolyticum genera in the Bacteriovoracaeae. Both families co-existed in ZDS compartments, constituting 0.13-1.4% of total Bacteria. Relative predator abundance varied according to the environmental conditions prevailing in different compartments, most notably salinity. Strikingly, the Bdellovibrionaceae, hitherto only retrieved from freshwater and soil, also populated the saline system. In addition to the detected BALOs, other potential predators were highly abundant, especially from the Myxococcales. Among the general bacterial population, Flavobacteria, Bacteroidetes, Fusobacteriaceae and unclassified Bacteria dominated a well mixed but seasonally fluctuating diverse community of up to 238 operational taxonomic units, as revealed by 16S rRNA gene sequencing.

Indigenous microbiota and habitat influence Escherichia coli survival more than sunlight in simulated aquatic environments

The reported fate of Escherichia coli in the environment ranges from extended persistence to rapid decline. Incomplete understanding of factors that influence survival hinders risk assessment and modeling of the fate of fecal indicator bacteria (FIB) and pathogens. FIB persistence in subtropical aquatic environments was explored in outdoor mesocosms inoculated with five E. coli strains. The manipulated environmental factors were (i) presence or absence of indigenous microbiota (attained by natural, disinfected, and cycloheximide treatments), (ii) freshwater versus seawater, and (iii) water column versus sediment matrices. When indigenous microbes were removed (disinfected), E. coli concentrations decreased little despite exposure to sunlight. Conversely, under conditions that included the indigenous microbiota (natural), significantly greater declines in E. coli occurred regardless of the habitat. The presence of indigenous microbiota and matrix significantly influenced E. coli decline, but their relative importance differed in freshwater versus seawater. Cycloheximide, which inhibits protein synthesis in eukaryotes, significantly diminished the magnitude of E. coli decline in water but not in sediments. The inactivation of protozoa and bacterial competitors (disinfected) caused a greater decline in E. coli than cycloheximide alone in water and sediments. These results indicate that the autochthonous microbiota are an important contributor to the decline of E. coli in fresh and seawater subtropical systems, but their relative contribution is habitat dependent. This work advances our understanding of how interactions with autochthonous microbiota influence the fate of E. coli in aquatic environments and provides the framework for studies of the ecology of enteric pathogens and other allochthonous bacteria in similar environments.

Differential decay of enterococci and Escherichia coli originating from two fecal pollution sources

Using in situ subtropical aquatic mesocosms, fecal source (cattle manure versus sewage) was shown to be the most important contributor to differential loss in viability of fecal indicator bacteria (FIB), specifically enterococci in freshwater and Escherichia coli in marine habitats. In this study, sunlight exposure and indigenous aquatic microbiota were also important contributors, whose effects on FIB also differed between water types.

Protist herbivory: a key pathway in the pelagic food web of Lake Tanganyika

Herbivory and bacterivory by phagotrophic protists were estimated in the southern basin of the oligotrophic Lake Tanganyika at different seasons (in the rainy season in February-March 2007 and in the dry season in July-August 2006 and September 2007), using two independent methods: the selective inhibitor technique for assessing community grazing on picocyanobacteria (PCya) and fluorescently labelled bacteria (FLB) and Synechococcus (FLA) to estimate bacterivory and herbivory by phagotrophic nanoflagellates (NF) and ciliates. Protistan grazing impact on both heterotrophic bacteria and PCya was mainly due to NF, which contributed up to 96% of the microbial grazing. There was a clear selection of FLA by protists. PCya represented the main carbon source for both flagellates and ciliates in the mixolimnion, accounting for an average of 83% of the total carbon obtained from the ingestion of picoplanktonic organisms. Protists were the main consumers of particulate primary production (46-74% depending on season). Significant seasonal variation of grazing rates (0.011-0.041 h(-1)) was found, chiefly following variation of PCya production and biomass. Assuming a growth efficiency of 0.4, total protozoan production varied seasonally (189-313 g C m(-2) day(-1)) and was roughly half of particulate phytoplankton production. This study provides evidence that NF and PCya were tightly coupled in Lake Tanganyika and that herbivory by protists may be one of the reasons why this great lake has high productivity. Our results bring support to the idea that microbial herbivory is a major process in oligotrophic freshwater systems.

When microbes and consumers determine the limiting nutrient of autotrophs: a theoretical analysis

Ecological stoichiometry postulates that differential nutrient recycling of elements such as nitrogen and phosphorus by consumers can shift the element that limits plant growth. However, this hypothesis has so far considered the effect of consumers, mostly herbivores, out of their food-web context. Microbial decomposers are important components of food webs, and might prove as important as consumers in changing the availability of elements for plants. In this theoretical study, we investigate how decomposers determine the nutrient that limits plants, both by feeding on nutrients and organic carbon released by plants and consumers, and by being fed upon by omnivorous consumers. We show that decomposers can greatly alter the relative availability of nutrients for plants. The type of limiting nutrient promoted by decomposers depends on their own elemental composition and, when applicable, on their ingestion by consumers. Our results highlight the limitations of previous stoichiometric theories of plant nutrient limitation control, which often ignored trophic levels other than plants and herbivores. They also suggest that detrital chains play an important role in determining plant nutrient limitation in many ecosystems.