Bacterially mediated removal of phosphorus and cycling of nitrate and sulfate in the waste stream of a "zero-discharge" recirculating mariculture system

Simultaneous removal of nitrogen and phosphorus by microbial biofilters has been used in a variety of water treatment systems including treatment systems in aquaculture. In this study, phosphorus, nitrate and sulfate cycling in the anaerobic loop of a zero-discharge, recirculating mariculture system was investigated using detailed geochemical measurements in the sludge layer of the digestion basin. High concentrations of nitrate and sulfate, circulating in the overlying water (~15 mM), were removed by microbial respiration in the sludge resulting in a sulfide accumulation of up to 3 mM. Modelling of the observed S and O isotopic ratios in the surface sludge suggested that, with time, major respiration processes shifted from heterotrophic nitrate and sulfate reduction to autotrophic nitrate reduction. The much higher inorganic P content of the sludge relative to the fish feces is attributed to conversion of organic P to authigenic apatite. This conclusion is supported by: (a) X-ray diffraction analyses, which pointed to an accumulation of a calcium phosphate mineral phase that was different from P phases found in the feces, (b) the calculation that the pore waters of the sludge were highly oversaturated with respect to hydroxyapatite (saturation index = 4.87) and (c) there was a decrease in phosphate (and in the Ca/Na molar ratio) in the pore waters simultaneous with an increase in ammonia showing there had to be an additional P removal process at the same time as the heterotrophic breakdown of organic matter

Eureka and beyond: mining's impact on African urbanisation

This collection brings separate literatures on mining and urbanisation together at a time when both artisanal and large-scale mining are expanding in many African economies. While much has been written about contestation over land and mineral rights, the impact of mining on settlement, notably its catalytic and fluctuating effects on migration and urban growth, has been largely ignored. African nation-states’ urbanisation trends have shown considerable variation over the past half century. The current surge in ‘new’ mining countries and the slow-down in ‘old’ mining countries are generating some remarkable settlement patterns and welfare outcomes. Presently, the African continent is a laboratory of national mining experiences. This special issue on African mining and urbanisation encompasses a wide cross-section of country case studies: beginning with the historical experiences of mining in Southern Africa (South Africa, Zambia, Zimbabwe), followed by more recent mineralizing trends in comparatively new mineral-producing countries (Tanzania) and an established West African gold producer (Ghana), before turning to the influence of conflict minerals (Angola, the Democratic Republic of Congo and Sierra Leone)

Soil nutrients and beta diversity in the Bornean Dipterocarpaceae: evidence for niche partitioning by tropical rain forest trees

1   The relative importance of niche- and dispersal-mediated processes in structuring diverse tropical plant communities remains poorly understood. Here, we link mesoscale beta diversity to soil variation throughout a lowland Bornean watershed underlain by alluvium, sedimentary and granite parent materials ( c . 340 ha, 8–200 m a.s.l.). We test the hypothesis that species turnover across the habitat gradient reflects interspecific partitioning of soil resources. 2   Floristic inventories (≥ 1 cm d.b.h.) of the Dipterocarpaceae, the dominant Bornean canopy tree family, were combined with extensive soil analyses in 30 (0.16 ha) plots. Six samples per plot were analysed for total C, N, P, K, Ca and Mg, exchangeable K, Ca and Mg, extractable P, texture, and pH. 3   Extractable P, exchangeable K, and total C, N and P varied significantly among substrates and were highest on alluvium. Thirty-one dipterocarp species ( n  = 2634 individuals, five genera) were recorded. Dipterocarp density was similar across substrates, but richness and diversity were highest on nutrient-poor granite and lowest on nutrient-rich alluvium. 4   Eighteen of 22 species were positively or negatively associated with parent material. In 8 of 16 abundant species, tree distribution (≥ 10 cm d.b.h.) was more strongly non-random than juveniles (1–10 cm d.b.h.), suggesting higher juvenile mortality in unsuitable habitats. The dominant species Dipterocarpus sublamellatus (> 50% of stems) was indifferent to substrate, but nine of 11 ‘subdominant’ species (> 8 individuals ha −1 ) were substrate specialists. 5   Eighteen of 22 species were significantly associated with soil nutrients, especially P, Mg and Ca. Floristic variation was significantly correlated with edaphic and geographical distance for all stems ≥ 1 cm d.b.h. in Mantel analyses. However, juvenile variation (1–10 cm d.b.h.) was more strongly related to geographical distance than edaphic factors, while the converse held for established trees (≥ 10 cm d.b.h.), suggesting increased importance of niche processes with size class. 6   Pervasive dipterocarp associations with soil factors suggest that niche partitioning structures dipterocarp tree communities. Yet, much floristic variation unrelated to soil was correlated with geographical distance between plots, suggesting that dispersal and niche processes jointly determine mesoscale beta diversity in the Bornean Dipterocarpaceae. Journal of Ecology (2005) doi: 10.1111/j.1365-2745.2005.01077.xPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72822/1/j.1365-2745.2005.01077.x.pd

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Floristic and faunal Cape biochoria: do they exist?

Many authors, over a long period, have remarked on the biotic distinctiveness of the southwestern corner of Africa, both in terms of its flora (Bolus 1886; White 1976; Goldblatt 1978) and its fauna (Moreau 1952; Stuckenberg 1962; Carcasson 1964; Poynton 1964; Holt et al. 2013). Climatically the region is defined by predominantly cool-season (autumn to spring) rainfall and mild temperatures (Chapter 2), and its plant species richness is unmatched in the rest of Africa (Manning and Goldblatt 2012; Snijman 2013). The Cape Floristic Region (CFR; or core Cape flora of Manning and Goldblatt 2012) is a distinctive phytogeographic feature (Goldblatt and Manning 2000), previously recognized as one of six global floral kingdoms on account of its high species richness and endemicity (Marloth 1908; Good 1974; Takhtajan 1986; but see Cox 2001 who considered this ranking untenable). More recently, the concept of a Greater Cape Floristic Region (GFCR), incorporating both the CFR and the succulent karoo region, has found favour as a more coherent biogeographical unit (Bayer 1984; Jürgens 1991, 1997; Born et al. 2007)

Linking size-dependent growth and mortality with architectural traits across 145 co-occurring tropical tree species

Tree architecture, growth, and mortality change with increasing tree size and associated light conditions. To date, few studies have quantified how size-dependent changes in growth and mortality rates co-vary with architectural traits, and how such size-dependent changes differ across species and possible light capture strategies. We applied a hierarchical Bayesian model to quantify size-dependent changes in demographic rates and correlated demographic rates and architectural traits for 145 co-occurring Malaysian rain-forest tree species covering a wide range of tree sizes. Demographic rates were estimated using relative growth rate in stem diameter (RGR) and mortality rate as a function of stem diameter. Architectural traits examined were adult stature measured as the 95-percentile of the maximum stem diameter (upper diameter), wood density, and three tree architectural variables: tree height, foliage height, and crown width. Correlations between demographic rates and architectural traits were examined for stem diameters ranging from 1 to 47 cm. As a result, RGR and mortality varied significantly with increasing stem diameter across species. At smaller stem diameters, RGR was higher for tall trees with wide crowns, large upper diameter, and low wood density. Increased mortality was associated with low wood density at small diameters, and associated with small upper diameter and wide crowns over a wide range of stem diameters. Positive correlations between RGR and mortality were found over the whole range of stem diameters, but they were significant only at small stem diameters. Associations between architectural traits and demographic rates were strongest at small stem diameters. In the dark understory of tropical rain forests, the limiting amount of light is likely to make the interspecific difference in the effects of functional traits on demography more clear. Demographic performance is therefore tightly linked with architectural traits such as adult stature, wood density, and capacity for horizontal crown expansion. The enhancement of a demographic trade-off due to interspecific variation in functional traits in the understory helps to explain species coexistence in diverse rain forest

Wood density explains architectural differentiation across 145 co-occurring tropical tree species

1. Because of its mechanical properties, wood density may affect the way that trees expand their stem and crown to exploit favourable light conditions in a mechanically stable way. From engineering theory and wood density properties, it is predicted that in terms of biomass investment, low-density wood is more efficient for vertical stem expansion, while high-density wood is more efficient for horizontal branch expansion. So far, these predictions have rarely been tested by empirical studies. 2. We tested these predictions for 145 co-occurring tree species in a Malaysian tropical rainforest. For each species, we selected trees across a broad size range and measured architectural dimensions (stem diameter, height of the lowest foliage and crown width). We used a hierarchical Bayesian model to estimate species-specific allometric relationships between architectural dimensions including estimated stem biomass. Then, we examined correlations between species wood density and estimated architectural variables at standardized heights. 3. When species were compared at standardized tree heights, wood density correlated negatively with stem diameter and positively with stem biomass at most reference heights. This indicates that species with low wood density produce thicker stems but at lower biomass costs. Wood density correlated positively with crown width and negatively with height of the lowest foliage, which indicates that high wood density species have wider and deeper crowns than low wood density species. These relationships were maintained at most reference heights. However, the relationship with crown width was nonsignificant above 18 m height. This may reflect large plastic response of lateral crown expansion to a local condition. 4. Wood density explains the trade-off between effective vertical stem expansion and horizontal crown expansion across co-occurring tropical tree species. Such mechanical constraints characterize the difference in tree architecture between low wood density species that show an efficient height expansion to attain better light conditions in the exposed canopy and high wood density species that show an efficient horizontal crown expansion to enhance current light interception and persistence in the shaded forest understorey. Our study thus suggests that the mechanical constraints set by wood density contribute to the co-existence of species differing in architecture and light capture strategy

Tree architecture and life-history strategies across 200 co-occurring tropical tree species

1. Tree architecture is thought to allow species to partition horizontal and vertical light gradients in the forest canopy. Tree architecture is closely related to light capture, carbon gain and the efficiency with which trees reach the canopy. Previous studies that investigated how light gradients drive differentiation in tree architecture have produced inconsistent results, partially because of the differences in which tree species and ontogenetic stages were studied. 2. We examined the relationship between stem diameter, tree height, foliage height, crown width and life-history strategy over a broad size range of 200 randomly selected, co-occurring tree species in a lowland rainforest in Peninsular Malaysia. We developed a hierarchical Bayesian model to account for both intra- and interspecific variation and describe the relationships among tree architectural variables. We analysed interspecific variation in tree architectural variables in relation to adult stature and light requirement for species regeneration as a function of tree size. 3. There was little interspecific variation in architectural variables, this is partly because of large intraspecific variation in response to canopy heterogeneity, but it also suggests architectural convergence within this community. However, interspecific analyses showed that, for large-statured species, small size classes had thinner stems with narrow and shallow crowns, whereas large-size classes had wider crowns. Light-demanding species (as indicated by high sapling mortality in shaded conditions) showed weak trends in tree architecture and were only characterized by wide crowns at intermediate sizes. 4. In summary, tree architectural traits overlapped across the species community. This suggests that architectural convergence and equalizing effects occur in this diverse tropical forest and that community-wide allometric equations can be used to describe forest height and carbon storage. Light resource partitioning also occurs, indicating stabilizing effects. Interspecific architectural variation in relation to adult stature supports the theory of the trade-off between early reproduction and vegetative growth. In closed rainforests, adult stature imposes a stronger force on architectural differentiation of species than regeneration light requirements