Detecting spatial hot spots in landscape ecology

Hot spots are typically locations of abundant phenomena. In ecology, hot spots are often detected with a spatially global threshold, where a value for a given observation is compared with all values in a data set. When spatial relationships are important, spatially local definitions – those that compare the value for a given observation with locations in the vicinity, or the neighbourhood of the observation – provide a more explicit consideration of space. Here we outline spatial methods for hot spot detection: kernel estimation and local measures of spatial autocorrelation. To demonstrate these approaches, hot spots are detected in landscape level data on the magnitude of mountain pine beetle infestations. Using kernel estimators, we explore how selection of the neighbourhood size (τ) and hot spot threshold impact hot spot detection. We found that as τ increases, hot spots are larger and fewer; as the hot spot threshold increases, hot spots become larger and more plentiful and hot spots will reflect coarser scale spatial processes. The impact of spatial neighbourhood definitions on the delineation of hot spots identified with local measures of spatial autocorrelation was also investigated. In general, the larger the spatial neighbourhood used for analysis, the larger the area, or greater the number of areas, identified as hot spots.     

Identification of proteins capable of metal reduction from the proteome of the Gram‐positive bacterium Desulfotomaculum reducens MI‐1 using an NADH‐based activity assay

Understanding of microbial metal reduction is based almost solely on studies of Gram‐negative organisms. In this study, we focus on Desulfotomaculum reducens MI‐1, a Gram‐positive metal reducer whose genome lacks genes with similarity to any characterized metal reductase. Using non‐denaturing separations and mass spectrometry identification, in combination with a colorimetric screen for chelated Fe(III)‐NTA reduction with NADH as electron donor, we have identified proteins from the D. reducens proteome not previously characterized as iron reductases. Their function was confirmed by heterologous expression in Escherichia coli. Furthermore, we show that these proteins have the capability to reduce soluble Cr(VI) and U(VI) with NADH as electron donor. The proteins identified are NADH : flavin oxidoreductase (Dred_2421) and a protein complex composed of oxidoreductase flavin adenine dinucleotide/NAD(P)‐binding subunit (Dred_1685) and dihydroorotate dehydrogenase 1B (Dred_1686). Dred_2421 was identified in the soluble proteome and is predicted to be a cytoplasmic protein. Dred_1685 and Dred_1686 were identified in both the soluble as well as the insoluble protein fraction, suggesting a type of membrane association, although PSORTb predicts both proteins are cytoplasmic. This study is the first functional proteomic analysis of D. reducens and one of the first analyses of metal and radionuclide reduction in an environmentally relevant Gram‐positive bacterium.     

Synthesis, characterization and crystal structure of the bimetallic cyano-bridged [(η-C5H5)(PPh3)2Ru(μ-CN)Ru(PPh3)2(η-C5H5)][PF6]

The bimetallic cyano-bridged [(η⁵-C₅H₅)(PPh₃)₂Ru(μ-CN)Ru(PPh₃)₂(η⁵-C₅H₅)][PF₆] (1) was prepared by reaction of [(η⁵-C₅H₅)(PPh₃)₂RuCl] with N,N′-bis(cyanomethyl)ethylenediamine. The single crystal structure determined by X-ray diffraction showed crystallization on the triclinic P1 space group with a perfect alignment of the cyanide bridges. This accentric crystallization was explored having in view the NLO properties at the macroscopic level, determined by the Kurtz Powder technique. Besides the very low efficiency values for the second harmonic generation, the value obtained for the bimetallic complex 1 showed to be higher than one of the parent complex [(η⁵-C₅H₅)(PPh₃)₂RuCN] (2).     

A single amino acid change restores DNA cytosine methyltransferase activity in a cloned chlorella virus pseudogene.

The chlorella virus PBCV-1 contains an open reading frame, named P17-ORF4, which differs by eight amino acids from a DNA cytosine methyltransferase, M.CviJI, encoded by a different chlorella virus IL-3A. Whereas IL-3A expresses M.CviJI, which methylates the central cytosine in (A/G)GC(T/C/G) sequences, P17-ORF4 is non-functional. Gene fusions between P17-ORF4 and M.CviJI and site-directed point mutations revealed that changing Gln188 to Lys188 abolishes M.CviJI methyltransferase activity. Conversely, changing Lys188 in P17-ORF4 to Gln188 results in M.CviJI activity. The other altered seven amino acids do not appear to affect M.CviJI activity.     

Genetic diversity of the black mangrove (Avicennia germinans L.) in Colombia

This study analyzed the genetic diversity and patterns of genetic structure in Colombian populations of Avicennia germinans L. using microsatellite loci. A lower genetic diversity was found on both the Caribbean (Ho = 0.439) and the Pacific coasts (Ho = 0.277) than reported for the same species in other locations of Central American Pacific, suggesting the deterioration of genetic diversity. All the populations showed high inbreeding coefficients (0.131–0.462) indicating heterozygotes deficience. The genetic structure between the Colombian coasts separated by Central American Isthmus was high (F_RT = 0.39) and the analyses of the genetic patterns of A. germinans revealed a clear differentiation of populations and no-recent gene flow evidence between coasts. Genetic structure was found within each coast (F_ST = 0.10 for the Caribbean coast and F_ST = 0.22 for the Pacific coast). The genetic patterns along the two coasts appear to reflect a forcing by local geomorphology and marine currents. Both coasts constitute a different Evolutionary Significant Unit, so we suggest for future transplantations plans that propagules or saplings of the populations of the Caribbean coast should not be mixed with those of the Pacific Colombian coast. Besides, we suggest that reforestation efforts should carefully distinguish propagules sources within each coast.     

Microbial tropicalization driven by a strengthening western ocean boundary current

Western boundary currents (WBCs) redistribute heat and oligotrophic seawater from the tropics to temperate latitudes, with several displaying substantial climate change‐driven intensification over the last century. Strengthening WBCs have been implicated in the poleward range expansion of marine macroflora and fauna, however, the impacts on the structure and function of temperate microbial communities are largely unknown. Here we show that the major subtropical WBC of the South Pacific Ocean, the East Australian Current (EAC), transports microbial assemblages that maintain tropical and oligotrophic (k‐strategist) signatures, to seasonally displace more copiotrophic (r‐strategist) temperate microbial populations within temperate latitudes of the Tasman Sea. We identified specific characteristics of EAC microbial assemblages compared with non‐EAC assemblages, including strain transitions within the SAR11 clade, enrichment of Prochlorococcus, predicted smaller genome sizes and shifts in the importance of several functional genes, including those associated with cyanobacterial photosynthesis, secondary metabolism and fatty acid and lipid transport. At a temperate time‐series site in the Tasman Sea, we observed significant reductions in standing stocks of total carbon and chlorophyll a, and a shift towards smaller phytoplankton and carnivorous copepods, associated with the seasonal impact of the EAC microbial assemblage. In light of the substantial shifts in microbial assemblage structure and function associated with the EAC, we conclude that climate‐driven expansions of WBCs will expand the range of tropical oligotrophic microbes, and potentially profoundly impact the trophic status of temperate waters.     

Introduction to "In Focus: Global Change and Adaptation in Local Places"

ABSTRACT   In recognition of unavoidable changes that human actions are producing in our environment, the term adaptation has become ubiquitous in the environmental and climate-change literature. Human adaptation is a field with a significant history in anthropology, yet anthropological contributions to the burgeoning field of climate change remain limited. This "In Focus" section presents studies of local adaptations to climate variation and change. Each is concerned with current environmental challenges and future environmental change, and each study is placed within a wider context that includes processes of globalization and integration into market economies, formal and informal institutions, and disasters. These studies highlight the challenges involved in understanding complex adaptations under conditions of stress. They also illustrate how anthropologists engage the larger climate-change and human-adaptation discussions and enhance our ability to respond to the challenges of a changing environment.