Divergent rainforest tree microbiomes between phases of the monsoon cycle, host plants and tissues.

The Australian Monsoon Tropics (AMT) contain some of the most biodiverse forests on the continent. Little is known about the dynamics of rainforest plant microbiomes in general, and there have been no community-level studies on Australian rainforest endophytes, their seasonality, tissue and host specificity. We tested whether community composition of tropical tree endophytes (fungi and bacteria) differs: (i) at different points during a monsoon cycle, (ii) between leaf and stem tissues, (iii) between forest microclimates (gully/ridge), and between (iv) host plant species, and (v) host plant clade, using amplicon sequencing of the bacterial 16S and fungal ITS2 gene regions. Results indicated that the composition of rainforest plant microbiomes differs between wet and dry seasons, which may be explained by physiological shifts in host plants due to annual climate fluctuations from mesic to xeric. Endophyte microbiomes differed between leaves and stems. Distinct fungal communities were associated with host species and clades, with some trees enriched in a number of fungal taxa compared to host plants in other clades. Diversity of bacterial endophytes in plant stems increased in the dry season. We conclude that the microbiomes of tropical plants are responsive to monsoonal climate variation, are highly compartmentalised between plant tissues, and may be partly shaped by the relatedness of their host plants.

Cross-Comparison of Human Wastewater-Associated Molecular Markers in Relation to Fecal Indicator Bacteria and Enteric Viruses in Recreational Beach Waters.

Detection of human wastewater contamination in recreational waters is of critical importance to regulators due to the risks posed to public health. To identify such risks, human wastewater-associated microbial source tracking (MST) markers have been developed. At present, however, a greater understanding of the suitability of these markers for the detection of diluted human wastewater in environmental waters is necessary to predict risk. Here, we compared the process limit of detection (PLOD) and process limit of quantification (PLOQ) of six human wastewater-associated MST markers (Bacteroides HF183 [HF183], Escherichia coli H8 [EC H8], Methanobrevibacter smithiinifH, human adenovirus [HAdV], human polyomavirus [HPyV], and pepper mild mottle virus [PMMoV]) in relation to a fecal indicator bacterium (FIB), Enterococcus sp. 23S rRNA (ENT 23S), and three enteric viruses (human adenovirus serotypes 40/41 [HAdV 40/41], human norovirus [HNoV], and human enterovirus [EV]) in beach water samples seeded with raw and secondary-treated wastewater. Among the six MST markers tested, HF183 was the most sensitive measure of human fecal pollution and was quantifiable up to dilutions of 10-6 and 10-4 for beach water samples seeded with raw and secondary-treated wastewater, respectively. Other markers and enteric viruses were detected at various dilutions (10-1 to 10-5). These MST markers, FIB, and enteric viruses were then quantified in beach water (n = 12) and sand samples (n = 12) from South East Queensland (SEQ), Australia, to estimate the levels of human fecal pollution. Of the 12 sites examined, beach water and sand samples from several sites had quantifiable concentrations of HF183 and PMMoV markers. Overall, our results indicate that while HF183 is the most sensitive measure of human fecal pollution, it should be used in conjunction with a conferring viral marker to avoid overestimating the risk of gastrointestinal illness.IMPORTANCE MST is an effective tool to help utilities and regulators improve recreational water quality around the globe. Human fecal pollution poses significant public health risks compared to animal fecal pollution. Several human wastewater-associated markers have been developed and used for MST field studies. However, a head-to-head comparison in terms of their performance to detect diluted human fecal pollution in recreational water is lacking. In this study, we cross-compared the performance of six human wastewater-associated markers in relation to FIB and enteric viruses in beach water samples seeded with raw and secondary-treated wastewater. The results of this study will provide guidance to regulators and utilities on the appropriate application of MST markers for tracking the sources of human fecal pollution in environmental waters and confer human health risks.

Isotopic evidence for the provenance and turnover of organic carbon by soil microorganisms in the Antarctic dry valleys.

The extremely cold and arid Antarctic dry valleys are one of the most environmentally harsh terrestrial ecosystems supporting organisms in which the biogeochemical transformations of carbon are exclusively driven by microorganisms. The natural abundance of (13)C and (15)N in source organic materials and soils have been examined to obtain evidence for the provenance of the soil organic matter and the C loss as CO(2) during extended incubation (approximately 1200 days at 10 degrees C under moist conditions) has been used to determine the potential decay of soil organic C. The organic matter in soils remote from sources of liquid water or where lacustrine productivity was low had isotope signatures characteristic of endolithic (lichen) sources, whereas at more sheltered and productive sites, the organic matter in the soils that was a mixture mainly lacustrine detritus and moss-derived organic matter. Soil organic C declined by up to 42% during extended incubation under laboratory conditions (equivalent to 50-73 years in the field on a thermal time basis), indicating relatively fast turnover, consistent with previous studies indicating mean residence times for soil organic C in dry valley soils in the range 52-123 years and also with recent inputs of relatively labile source materials.

Field evaluation of in situ remediation of a heavy metal contaminated soil using lime and red-mud.

We evaluated the effectiveness of lime and red mud (by-product of aluminium manufacturing) to reduce metal availability to Festuca rubra and to allow re-vegetation on a highly contaminated brown-field site. Application of both lime and red mud (at 3 or 5%) increased soil pH and decreased metal availability. Festuca rubra failed to establish in the control plots, but grew to a near complete vegetative cover on the amended plots. The most effective treatment in decreasing grass metal concentrations in the first year was 5% red mud, but by year two all amendments were equally effective. In an additional pot experiment, P application in combination with red mud or lime decreased the Pb concentration, but not total uptake of Pb in Festuca rubra compared to red mud alone. The results show that both red mud and lime can be used to remediate a heavily contaminated acid soil to allow re-vegetation.

Relationship of early readings of minimal inhibitory concentrations to the results of overnight tests.

Broth dilution minimal inhibitory concentration (MIC) readings were compared after different incubation periods and with different inoculum concentrations. The purpose was to determine the best conditions for obtaining early results as close as possible to overnight readings. Initially, 76 antibiotic-organism combinations were tested using the International Collaborative Study technique and inoculum and were read after 3, 8, and 18 h of incubation. Approximately 28% of tests showed fourfold or greater increases in MICs after 18 h of incubation compared with the 3-h readings. No overnight MICs were lower than early readings. MICs of single antibiotics against seven organisms were also read with an automatic particle counter to confirm the validity of the visual readings. Experiments were made to determine whether inoculum manipulation could reconcile the differences between 3- and 18-h MIC results. One hundred and eight organism-antibiotic combinations were tested comparing 3-h MIC readings using an inoculum of 10(7) organisms per ml with overnight readings using 10(5) per ml. In 71 cases, readings with both inocula were within the range tested and 57 (86%) were within +/-1 log(2) of each other and followed an approximately normal distribution. Improved comparability between early read and overnight MICs thus may be achieved by inoculum manipulation, and this may be a suitable approach in the future development of automated procedures.