Aims:  The goal of this study was to develop and test the efficacy of a PCR assay for the environmental detection of the nifH gene of Methanobrevibacter smithii, a methanogen found in human faeces and sewage. Methods and Results:  PCR primers for the nifH gene of M. smithii were designed, tested and used to detect the presence or absence of this organism in faecal and environmental samples. Specificity analysis showed that the Mnif primers amplified products only in M. smithii pure culture strains (100%), human faeces (29%), human sewage samples (93%) and sewage‐contaminated water samples (100%). No amplification was observed when primers were tested against 43 bacterial stock cultures, 204 animal faecal samples, 548 environmental bacterial isolates and water samples from a bovine waste lagoon and adjacent polluted creek. Sequencing of PCR products from sewers demonstrated that a 222‐bp product was the nifH gene of M. smithii. The minimal amount of total DNA required for the detection of M. smithii was 10 ng for human faeces, 10 ng for faecally contaminated water and 5 ng for sewage. Recreational water seeded with M. smithii established a lower detection limit of 13 cells ml−1. Conclusions:  The Mnif assay developed during this investigation showed successful detection of M. smithii in individual human faecal samples, sewage and sewage‐contaminated water but not in uncontaminated marine water or bovine‐contaminated waters. The Mnif assay appears to be a potentially useful method to detect sewage‐polluted coastal waters. Significance and Impact of the Study:  This study was the first to utilize methanogens as an indicator of sewage pollution. Mnif PCR detection of M. smithii was shown to be a rapid, inexpensive and reliable test for determining the presence or absence of sewage pollution in coastal recreational waters.

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Although the gut microbiota is known to provide many beneficial functions to animal hosts, such as aiding in digestion, fat metabolism, and immune function, relatively little is known about the gut microbiota of passerines. Gut microbes may have both beneficial and detrimental impacts on the fitness of migratory passerines; however physiological and morphological changes associated with prolonged migratory flight may cause disruptions of the stable microbiota and potentially a loss of function. Fecal samples were collected from Swainson's thrushes Catharus ustulatus and gray catbirds Dumetella carolinensis immediately after crossing the Gulf of Mexico during spring migration and before crossing during fall, and microbiota communities were analyzed using next‐generation sequencing. Microbiota communities were generally dominated by Firmicutes and Proteobacteria, with potential pathogens as well as potentially beneficial bacteria identified in all birds. Energetic condition of migrants was not significantly related to overall microbiota community structure though it cannot be conclusively stated that migratory flight does not impact the microbiota. Spring and fall migrants showed clear differences in microbiota communities, indicating that environmental factors influence the gut microbiota of these species more than host genetics.

Although some species of fish, crustaceans, and molluscs may behaviorally avoid hypoxic masses of small size and limited duration, others cannot. In a series of crustaceans, tolerance of hypoxia over 28 days at 30C, decreases as follows: Eurypanopeus depressus (38 Torr = LC 50 ) > Palae monetes pugio > Rhithropanopeus harrisii > Penaeus aztecus > Callinectes sapidus (121 Torr = LC 50 ). Callinectes sapidus and E. depressus die during 1 2-h exposure to anoxia and their heat dissipation rates (quantified by microcalorimetry) are depressed in seawater at 25% air saturation (normoxia) to only 32 and 47% of their metabolic rate at normoxia. In contrast, starved Crassostrea virginica and Thais haemastorna are anoxia tolerant; their metabolic rates are depressed under anoxia to 75% and 9% of the normoxic rate. Hypoxia tolerance is greater at 20C than at 30C for Penaeus aztecus and Crassostrea virginica, but no temperature effect on tolerance exists for Callinectes sapidus. Hypoxia tolerance varies inversely with salinity for Penaeus aztecus at 20 and 30C and for Callinectes sapidus at 30C, but it varies directly with salinity at 20C in Callinectes sapidus. Greater depression of metabolic rate occurs in molluscs during anoxia exposure (and is correlated with greater hypoxia tolerance) than occurs in Callinectes sapidus and Penaeus aztecus, which are not anoxia tolerant. Heavy mortality probably occurs in young Callinectes sapidus and Penaeus aztecus and in

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Both positive and negative interactions among bacteria take place in the environment. We hypothesize that the complexity of the substrate affects the way bacteria interact with greater cooperation in the presence of recalcitrant substrate. We isolated lignocellulolytic bacteria from salt marsh detritus and compared the growth, metabolic activity and enzyme production of pure cultures to those of three-species mixed cultures in lignocellulose and glucose media. Synergistic growth was common in lignocellulose medium containing carboxyl methyl cellulose, xylan and lignin but absent in glucose medium. Bacterial synergism promoted metabolic activity in synergistic mixed cultures but not the maximal growth rate (μ). Bacterial synergism also promoted the production of β-1,4-glucosidase but not the production of cellobiohydrolase or β-1,4-xylosidase. Our results suggest that the chemical complexity of the substrate affects the way bacteria interact. While a complex substrate such as lignocellulose promotes positive interactions and synergistic growth, a labile substrate such as glucose promotes negative interactions and competition. Synergistic interactions among indigenous bacteria are suggested to be important in promoting lignocellulose degradation in the environment.

• Premise of the study: PCR amplification of DNA extracted from plants is sometimes difficult due to the presence of inhibitory compounds. An effective method to overcome the inhibitory effect of compounds that contaminate DNA from difficult plant specimens is needed.• Methods and Results: The effectiveness of a PCR additive reagent containing trehalose, bovine serum albumin (BSA), and polysorbate-20 (Tween-20) (TBT-PAR) was tested. PCR of DNA extracted from fresh, silica-dried, and herbarium leaf material of species of Achariaceae, Asteraceae, Lacistemataceae, and Samydaceae that failed using standard techniques were successful with the addition of TBT-PAR.• Conclusions: The addition of TBT-PAR during routine PCR is an effective method to improve amplification of DNA extracted from herbarium specimens or plants that are known to contain PCR inhibitors.