Microbial source tracking (MST) describes a suite of methods and an investigative strategy for determination of fecal pollution sources in environmental waters that rely on the association of certain fecal microorganisms with a particular host. MST is used to assess recreational water quality and associated human health risk, and total maximum daily load allocations. Many methods rely on signature molecules (markers) such as DNA sequences of host-associated microorganisms. Human sewage pollution is among the greatest concerns for human health due to (1) the known risk of exposure to human waste and (2) the public and regulatory will to reduce sewage pollution; however, methods to identify animal sources are receiving increasing attention as our understanding of zoonotic disease potential improves. Here, we review the performance of MST methods in initial reports and field studies, with particular emphasis on quantitative PCR (qPCR). Relationships among human-associated MST markers, fecal indicator bacteria, pathogens, and human health outcomes are presented along with recommendations for future research. An integrated understanding of the advantages and drawbacks of the many MST methods targeting human sources advanced over the past several decades will benefit managers, regulators, researchers, and other users of this rapidly growing area of environmental microbiology.

BackgroundThe sinorhizobia are amongst the most well studied members of nitrogen-fixing root nodule bacteria and contribute substantial amounts of fixed nitrogen to the biosphere. While the alfalfa symbiont Sinorhizobium meliloti RM 1021 was one of the first rhizobial strains to be completely sequenced, little information is available about the genomes of this large and diverse species group.ResultsHere we report the draft assembly and annotation of 48 strains of Sinorhizobium comprising five genospecies. While S. meliloti and S. medicae are taxonomically related, they displayed different nodulation patterns on diverse Medicago host plants, and have differences in gene content, including those involved in conjugation and organic sulfur utilization. Genes involved in Nod factor and polysaccharide biosynthesis, denitrification and type III, IV, and VI secretion systems also vary within and between species. Symbiotic phenotyping and mutational analyses indicated that some type IV secretion genes are symbiosis-related and involved in nitrogen fixation efficiency. Moreover, there is a correlation between the presence of type IV secretion systems, heme biosynthesis and microaerobic denitrification genes, and symbiotic efficiency.ConclusionsOur results suggest that each Sinorhizobium strain uses a slightly different strategy to obtain maximum compatibility with a host plant. This large genome data set provides useful information to better understand the functional features of five Sinorhizobium species, especially compatibility in legume-Sinorhizobium interactions. The diversity of genes present in the accessory genomes of members of this genus indicates that each bacterium has adopted slightly different strategies to interact with diverse plant genera and soil environments.

Bacteria and fungi are important mediators of biogeochemical processes and play essential roles in the establishment of plant communities, which makes knowledge about their recovery after extreme disturbances valuable for understanding ecosystem development. However, broad ecological differences between bacterial and fungal organisms, such as growth rates, stress tolerance, and substrate utilization, suggest they could follow distinct trajectories and show contrasting dynamics during recovery. In this study, we analyzed both the intra-annual variability and decade-scale recovery of bacterial and fungal communities in a chronosequence of reclaimed mined soils using next-generation sequencing to quantify their abundance, richness, ␤-diversity, taxonomic composition, and cooccurrence network properties. Bacterial communities shifted gradually, with overlapping ␤-diversity patterns across chronosequence ages, while shifts in fungal communities were more distinct among different ages. In addition, the magnitude of intra-annual variability in bacterial ␤-diversity was comparable to the changes across decades of chronosequence age, while fungal communities changed minimally across months. Finally, the complexity of bacterial cooccurrence networks increased with chronosequence age, while fungal networks did not show clear age-related trends. We hypothesize that these contrasting dynamics of bacteria and fungi in the chronosequence result from (i) higher growth rates for bacteria, leading to higher intra-annual variability; (ii) higher tolerance to environmental changes for fungi; and (iii) stronger influence of vegetation on fungal communities. IMPORTANCE Both bacteria and fungi play essential roles in ecosystem functions, and information about their recovery after extreme disturbances is important for understanding whole-ecosystem development. Given their many differences in phenotype, phylogeny, and life history, a comparison of different bacterial and fungal recovery patterns improves the understanding of how different components of the soil microbiota respond to ecosystem recovery. In this study, we highlight key differences between soil bacteria and fungi during the restoration of reclaimed mine soils in the form of long-term diversity patterns, intra-annual variability, and potential interaction networks. Cooccurrence networks revealed increasingly complex bacterial community interactions during recovery, in contrast to much simpler and more isolated fungal network patterns. This study compares bacterial and fungal cooccurrence networks and reveals cooccurrences persisting through successional ages.KEYWORDS bacteria, chronosequence, cooccurrence networks, disturbance, fungi, reclaimed mine soils, soil microbiota E cologists have been studying the succession dynamics of plant communities for more than a century (1, 2), and the patterns of changes in plant community composition are used as indicators for the restoration of ecosystems (3-5). However,

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Elevated concentrations of fecal indicator bacteria (FIB) in aquatic sediments and vegetation have prompted concern that environmental reservoirs of FIB disrupt the correlation between indicator organisms, pathogens and human health risks. FIB numbers, however, are typically normalized to volume of water or mass of substrate. Because these reservoirs tend to differ greatly in magnitude within and between water bodies, direct comparison between water column and benthic population sizes can be problematic. Normalization to a set volume of water or mass of substrate, e.g. cfu (100 ml)(-1) or cfu(100 g)(-1), can give a false picture of the relative contributions of various reservoirs to FIB numbers across the ecosystem, and of the potential for FIBs to trigger health advisories as they pass from one reservoir to another. Here, we normalized enterococci concentrations from water, sediment and submerged aquatic vegetation (SAV) to land surface area (m(2) ) to compare their relative importance in the entire system. SAV-associated enterococci comprised only 0-18% of the entire population, even though they displayed the highest concentrations of enterococci per unit mass. The largest proportion of the enterococci population was in the water column (4-77%) or sediments (20-95%), depending on the volume of each substrate available at a site and FIB concentrations within them. Models indicated that large shifts in the relative size of FIB populations in each substrate can result from changes in per cent SAV cover, water depth and depth of sediment colonization. It follows that high concentrations of FIB in sediments or SAV do not necessarily signify large environmental reservoirs of FIB that can affect the water column. Comprehensive analyses that include FIB measurements from water, SAV and sediment normalized to land surface area offer a more balanced perspective on total FIB numbers contained in various matrices of an aquatic system.

Despite a nationwide emphasis on improving soil health in the United States, current measurement protocols have little consistency. To survey assessment practices, we conducted a meta-analysis of cover crop (n = 86) and no-tillage (n = 106) studies and compiled reported indicators, cropping systems, and soil sampling protocols from each. We then analyzed which indicators signiicantly responded to cover crop usage after 1 yr and 2 to 3 yr. Our results showed that out of 42 indicators, only 8 were reported in >20% of studies. Thirteen indicators showed >10% relative response after 1 to 3 yr; the remainder lacked either suicient observations or consistent results. Looking forward, we propose that emphasis should be placed on (i) pursuing dynamic indicators (e.g., aggregate stability), (ii) standardizing sampling protocols, and (iii) developing a common framework for information sharing. These eforts will generate new insight into soil health across systems, ultimately ensuring that soil health science is useful to producers and regulators.

The nitritation-anammox process has been a promising nitrogen removal technology towards sustainable wastewater treatment, but its application in treating domestic wastewater with relatively low ammonium concentrations (mainstream) remains a great challenge. In this study, an innovative lab-scale upflow membrane-aerated biofilm reactor (UMABR) was employed to treat a synthetic wastewater containing 70 mg N L(-1) ammonium. With a DO level at 0.6 ± 0.1 mg O2 L(-1) and HRT of 32 h, the effluent ammonium concentration was 4.8 ± 2.0 mg N L(-1). Increasing the nitrogen loading rate from 52.4 to 104.8 g N m(-3) d(-1) with stepwise decreasing HRT from 32 to 16 h resulted in an average TN removal efficiency of 81% without nitrite accumulation. The average observed NO3(-)-N (residue)/NH4(+)-N (consumed) ratio of 8% was below the "theoretical ratio" of 13% and further reduction of nitrate residue needs to be addressed. Fluorescence in situ hybridization (FISH) and high-throughput sequencing analyses showed the coexistence of anammox bacteria and ammonium-oxidizing bacteria (AOB) in both biofilm and granular samples. Anammox bacteria accounted for up to 63.3% of the microbial community of the granules, with Candidatus Jettenia being the distinctly dominant anammox genus. In contrast, the biofilm contained abundant Nitrosomonadaceae (AOB, 33.1%). In addition, the brown-yellow granules exhibited a more balanced community structure with anammox bacteria and AOB accounting for 33.7% and 18.2%, respectively, which may contribute to the long-term operation of single-stage nitritation-anammox process. These results demonstrate that the nitritation-anammox UMABR could potentially be used for nitrogen removal from mainstream in some specific regions with relatively warm temperature.

Enterococcus spp. are utilized worldwide as faecal indicator bacteria, but certain strains exhibit extended survival in environmental habitats and the factors influencing their persistence are poorly understood. We used flowing freshwater mesocosms to explore the effect of submerged aquatic vegetation (SAV) on the persistence of natural enterococci populations from a subtropical lake. The highest mean densities of culturable enterococci over 2 weeks occurred in SAV [8.6 x 10(2) colony-forming units (cfu) per 100 g wet weight], followed by sediments (1.3 x 10(2) cfu per 100 g) and water (18 cfu per 100 ml). However, due to relative differences in the total mass of each substrate in the entire system (water > sediments > SAV), SAV-associated enterococci represented only a minor proportion of the total population. Vegetated mesocosms harboured significantly higher mean cfu per mesocosm and cfu densities in sediments compared with their unvegetated counterparts, suggesting that SAV indirectly facilitates persistence in aquatic habitats. Populations were dominated (> 96%) by a single Enterococcus casseliflavus strain according to BOX-PCR genotyping, which did not change over the 10-month study and strongly suggests bacterial replication in the lake. The presence of such strains in the environment may represent highly competitive, naturalized and reproducing indicator bacteria populations that are not directly related to pollution events.