Thomas C. J. Hill

Using ecological diversity measures with bacterial communities

Abstract There are many ecological diversity measures, but their suitability for use with highly diverse bacterial communities is unclear and seldom considered. We assessed a range of species richness and evenness/dominance indices, and the use of species abundance models using samples of bacteria from zinc-contaminated and control soils. Bacteria were assigned to operational taxonomic units (OTUs) using amplified ribosomal DNA restriction analysis of 236 clones from each soil. The reduced diversity apparent in the contaminated soil was reflected by the diversity indices to varying degrees. The number of clones analysed and the weighting given to rare vs. abundant OTUs are the most important considerations when selecting measures. Our preferences, arrived at using theory and practical experience, include: the log series index alpha; the Q statistic (but only if coverage is 50% or more); the Berger-Parker and Simpsons indices, although their ecological relevance may be limited; and, unexpectedly, the Shannon-Wiener and Shannon evenness indices, even though their meanings may not be clear and their values inaccurate when coverage is low. For extrapolation, the equation for the log series distribution seems the best for extrapolating from OTU accumulation curves while non-parametric methods, such as Chao 1, show promise for estimating total OTU richness. Due to a preponderance of single-occurrence OTUs, none of the five species abundance models fit the OTU abundance distribution of the control soil, but both the log and log normal models fit the less diverse contaminated soil. Species abundance models are useful, irrespective of coverage, because they address the whole distribution of a sample, aiding comparison by revealing overall trends as well as specific changes in particular abundance classes.

The utility of ergosterol as a bioindicator of fungi in temperate soils

In this paper we evaluate the utility of ergosterol as a measure of fungal biomass in temperate soils. We summarise published findings and compare them with data from our own broad-scale assessment of the relationship between ergosterol and ATP in a range of temperate soils. Two hundred and ninety five plots (three cores taken from each 10 × 10 m plot) in seven ecotypes were sampled. Soils ranged from entirely mineral to entirely organic (0.01–46% Corg) and sites comprised two primary successions, one on shingle ridge on the south coast of England and one in the slack of a dune blow-out on the south coast of Wales, various meadow, pasture (some restored after opencast mining) and ancient woodland soils throughout England and acid forest soils in Central Europe. We found a strong relationship between ergosterol and ATP (r2=0.80), which was largely unaffected by the key soil properties of Corg, C/N ratio, moisture and pH. The sources and implications of the 20% of residual variance were explored by assuming that the error was compounded from three sources: the inaccuracies in methods of analysis of ergosterol and ATP, the failings of each of the variables to estimate their underlying populations (i.e., fungal and total biomass, respectively) (evar), and the non-equivalence of these populations (i.e., their incomplete overlap) (epop). By partitioning the residual variance into components corresponding to the levels of sampling, we estimated that the sum of the systematic portions of evar and epop formed as much as three quarters of the 20% of residual variance in the ATP–ergosterol correlation, leaving just 5% mostly due to random error. Despite this close relationship, the attainment of a universal conversion factor between ergosterol and fungal biomass, applicable to all temperate soils, remains elusive and problematic. Many problems are caused by a lack of comparability between the various measures of fungal and total biomass used and the reliability, or otherwise, of extrapolations based on measures of axenic cultures (in contrast to in-situ measurements). The issue is further complicated by the non-linearity of the relationship between fungal biomass and fungal surface area; ergosterol is more correctly an index of the latter since it is a principal membrane sterol. We conclude that ergosterol is likely to be a reliable indicator of the extent of fungal membranes in temperate soils, if not an accurate measure of fungal biomass.

Zinc contamination decreases the bacterial diversity of agricultural soil

Abstract Around half a million tonnes of biosolids (sewage sludge dry solids) are applied to agricultural land in the United Kingdom each year, and this may increase to 732 000 t by 2005/6. The heavy metals contained in biosolids may permanently degrade the microbial decomposer communities of agricultural soils. We used amplified ribosomal DNA restriction analysis of the extractable bacterial fraction to compare the diversity of a zinc-contaminated soil (400 mg kg(-1) Zn; pH 5.7 and 1.36% C(org)) with that of a control soil (57 mg kg(-1) Zn; pH 6.2 and 1.40% C(org)) from a long-term sewage sludge experiment established in 1982 at ADAS Gleadthorpe. Comparison of the restriction fragment length polymorphisms of 236 clones from each soil suggested that the stress caused by zinc toxicity had lowered bacterial diversity. There were 120 operational taxonomic units (OTUs) in the control soil, but only 90 in the treated soil, a decrease of 25%. While the control soil had 82 single-occurrence OTUs the contaminated soil had only 52. The fall in diversity was accompanied by a decrease in evenness. The most abundant OTUs in the contaminated soil (which tended to be common to both soils) accounted for a higher proportion of clones than in the control. The most dominant OTU, in both soils, belonged to the Rubrobacter radiotolerans group of the high G+C Gram-positive bacteria. The data was also used to develop efficient sampling strategies.

Sea spray aerosol as a unique source of ice nucleating particles

Ice nucleating particles (INPs) are vital for ice initiation in, and precipitation from, mixed-phase clouds. A source of INPs from oceans within sea spray aerosol (SSA) emissions has been suggested in previous studies but remained unconfirmed. Here, we show that INPs are emitted using real wave breaking in a laboratory flume to produce SSA. The number concentrations of INPs from laboratory-generated SSA, when normalized to typical total aerosol number concentrations in the marine boundary layer, agree well with measurements from diverse regions over the oceans. Data in the present study are also in accord with previously published INP measurements made over remote ocean regions. INP number concentrations active within liquid water droplets increase exponentially in number with a decrease in temperature below 0 °C, averaging an order of magnitude increase per 5 °C interval. The plausibility of a strong increase in SSA INP emissions in association with phytoplankton blooms is also shown in laboratory simulations. Nevertheless, INP number concentrations, or active site densities approximated using “dry” geometric SSA surface areas, are a few orders of magnitude lower than corresponding concentrations or site densities in the surface boundary layer over continental regions. These findings have important implications for cloud radiative forcing and precipitation within low-level and midlevel marine clouds unaffected by continental INP sources, such as may occur over the Southern Ocean.

Microbial Control of Sea Spray Aerosol Composition: A Tale of Two Blooms.

With the oceans covering 71% of the Earth, sea spray aerosol (SSA) particles profoundly impact climate through their ability to scatter solar radiation and serve as seeds for cloud formation. The climate properties can change when sea salt particles become mixed with insoluble organic material formed in ocean regions with phytoplankton blooms. Currently, the extent to which SSA chemical composition and climate properties are altered by biological processes in the ocean is uncertain. To better understand the factors controlling SSA composition, we carried out a mesocosm study in an isolated ocean-atmosphere facility containing 3,400 gallons of natural seawater. Over the course of the study, two successive phytoplankton blooms resulted in SSA with vastly different composition and properties. During the first bloom, aliphatic-rich organics were enhanced in submicron SSA and tracked the abundance of phytoplankton as indicated by chlorophyll-a concentrations. In contrast, the second bloom showed no enhancement of organic species in submicron particles. A concurrent increase in ice nucleating SSA particles was also observed only during the first bloom. Analysis of the temporal variability in the concentration of aliphatic-rich organic species, using a kinetic model, suggests that the observed enhancement in SSA organic content is set by a delicate balance between the rate of phytoplankton primary production of labile lipids and enzymatic induced degradation. This study establishes a mechanistic framework indicating that biological processes in the ocean and SSA chemical composition are coupled not simply by ocean chlorophyll-a concentrations, but are modulated by microbial degradation processes. This work provides unique insight into the biological, chemical, and physical processes that control SSA chemical composition, that when properly accounted for may explain the observed differences in SSA composition between field studies.

Measurement of Ice Nucleation-Active Bacteria on Plants and in Precipitation by Quantitative PCR

ABSTRACT Ice nucleation-active (INA) bacteria may function as high-temperature ice-nucleating particles (INP) in clouds, but their effective contribution to atmospheric processes, i.e., their potential to trigger glaciation and precipitation, remains uncertain. We know little about their abundance on natural vegetation, factors that trigger their release, or persistence of their ice nucleation activity once airborne. To facilitate these investigations, we developed two quantitative PCR (qPCR) tests of the ina gene to directly count INA bacteria in environmental samples. Each of two primer pairs amplified most alleles of the ina gene and, taken together, they should amplify all known alleles. To aid primer design, we collected many new INA isolates. Alignment of their partial ina sequences revealed new and deeply branching clades, including sequences from Pseudomonas syringae pv. atropurpurea, Ps. viridiflava, Pantoea agglomerans, Xanthomonas campestris, and possibly Ps. putida, Ps. auricularis, and Ps. poae. qPCR of leaf washings recorded ∼108 ina genes g−1 fresh weight of foliage on cereals and 105 to 107 g−1 on broadleaf crops. Much lower populations were found on most naturally occurring vegetation. In fresh snow, ina genes from various INA bacteria were detected in about half the samples but at abundances that could have accounted for only a minor proportion of INP at −10°C (assuming one ina gene per INA bacterium). Despite this, an apparent biological source contributed an average of ∼85% of INP active at −10°C in snow samples. In contrast, a thunderstorm hail sample contained 0.3 INA bacteria per INP active at −10°C, suggesting a significant contribution to this sample.

Microbial biomass estimated by phospholipid phosphate in soils with diverse microbial communities

Phospholipid phosphate (PL-P) was tested as a measure of total microbial biomass in diverse soils with varying relative abundances of fungi. Phospholipid concentrations were compared with adenosine triphosphate (ATP), ergosterol, dehydrogenase activity, organic carbon and total N concentration. PL-P varied from 6 nmol g−1 in recently colonized dune sand to 1500 nmol g−1 in humus sieved from the pebbles of shingle ridge grassland. Meadow soils ranged from 340 nmol g−1 in arable land to 660 nmol g−1 in species-rich floodmeadow. Phospholipid phosphate correlated well with ATP (r2=0.80 or 0.93 minus one outlier, P < 0.001), total N (r2 =0.84, P < 0.001) and, negatively, with C:N ratio (r2 = 0.73, P < 0.001). The close relationship with N may reflect its limiting influence in sites that were mostly transitional stages within primary or old-field successions. A biomass conversion ratio of 419 ± 62 (SE) nmol PL-P mg−1 biomass C was estimated assuming 5.93 μg ATP mg−1 biomass C. Contrary to prediction, PL-P content of the microbial biomass did not fall with increasing fungal proportion; the PL-P: ATP molar ratio did not decrease with an increase in ergosterol: ATP molar ratio.

Characteristics of atmospheric ice nucleating particles associated with biomass burning in the US: Prescribed burns and wildfires

An improved understanding of atmospheric ice nucleating particles (INP), including sources and atmospheric abundance, is needed to advance our understanding of aerosol-cloud-climate interactions. This study examines diverse biomass burning events to better constrain our understanding of how fires impact populations of INP. Sampling of prescribed burns and wildfires in Colorado and Georgia, U.S.A., revealed that biomass burning leads to the release of particles that are active as condensation/immersion freezing INP at temperatures from −32 to −12°C. During prescribed burning of wiregrass, up to 64% of INP collected during smoke-impacted periods were identified as soot particles via electron microscopy analyses. Other carbonaceous types and mineral-like particles dominated INP collected during wildfires of ponderosa pine forest in Colorado. Total measured nINP and the excess nINP associated with smoke-impacted periods were higher during two wildfires compared to the prescribed burns. Interferences from non-smoke sources of INP, including long-range transported mineral dust and local contributions of soils and plant materials lofted from the wildfires themselves, presented challenges in using the observations to develop a smoke-specific nINP parameterization. Nevertheless, these field observations suggest that biomass burning may serve as an important source of INP on a regional scale, particularly during time periods that lack other robust sources of INP such as long-range transported mineral dust.

The recent invasion of natural Drosophila simulans populations by the P-element

Significance Transposable elements (TEs) persist via two evolutionary strategies—in the short term, they selfishly propagate within genomes, and over the long term, they spread horizontally between species. Famously, the P-element invaded Drosophila melanogaster populations some time before 1950 and spread rapidly worldwide. Here, we show that it has also invaded a close relative, Drosophila simulans, from which it was absent until recently. The genomic tools at our disposal offer the unique opportunity to study the dynamics of a TE invasion at multiple levels and to compare the spread of the P-element in D. simulans with the well-investigated invasion of D. melanogaster. The P-element is one of the best understood eukaryotic transposable elements. It invaded Drosophila melanogaster populations within a few decades but was thought to be absent from close relatives, including Drosophila simulans. Five decades after the spread in D. melanogaster, we provide evidence that the P-element has also invaded D. simulans. P-elements in D. simulans appear to have been acquired recently from D. melanogaster probably via a single horizontal transfer event. Expression data indicate that the P-element is processed in the germ line of D. simulans, and genomic data show an enrichment of P-element insertions in putative origins of replication, similar to that seen in D. melanogaster. This ongoing spread of the P-element in natural populations provides a unique opportunity to understand the dynamics of transposable element spread and the associated piwi-interacting RNAs defense mechanisms.

A Dynamic Link between Ice Nucleating Particles Released in Nascent Sea Spray Aerosol and Oceanic Biological Activity during Two Mesocosm Experiments

AbstractEmission rates and properties of ice nucleating particles (INPs) are required for proper representation of aerosol–cloud interactions in atmospheric models. Few investigations have quantified marine INP emissions, a potentially important INP source for remote oceanic regions. Previous studies have suggested INPs in sea spray aerosol (SSA) are linked to oceanic biological activity. This proposed link was explored in this study by measuring INP emissions from nascent SSA during phytoplankton blooms during two mesocosm experiments. In a Marine Aerosol Reference Tank (MART) experiment, a phytoplankton bloom was produced with chlorophyll-a (Chl a) concentrations reaching 39 μg L−1, while Chl a concentrations more representative of natural ocean conditions were obtained during the Investigation into Marine Particle Chemistry and Transfer Science (IMPACTS; peak Chl a of 5 μg L−1) campaign, conducted in the University of California, San Diego, wave flume. Dynamic trends in INP emissions occurred for INPs ...