Fungi are the principal degraders of biomass in most terrestrial ecosystems. In contrast to surface environments, deep-sea environmental gene libraries have suggested that fungi are rare and non-diverse in high-pressure marine environments. Here, we report the diversity of fungi from 11 deep-sea samples from around the world representing depths from 1500 to 4000 m (146-388 atm) and two shallower water column samples (250 and 500 m). We sequenced 239 clones from 10 fungal-specific 18S rRNA gene libraries constructed from these samples, from which we detected only 18 fungal 18S-types in deep-sea samples. Our phylogenetic analyses show that a total of only 32 fungal 18S-types have so far been recovered from deep-sea habitats, and our results suggest that fungi, in general, are relatively rare in the deep-sea habitats we sampled. The fungal diversity detected suggests that deep-sea environments host an evolutionarily diverse array of fungi dominated by groups of distantly related yeasts, although four putative filamentous fungal 18S-types were detected. The majority of our new sequences branch close to known fungi found in surface environments. This pattern contradicts the proposal that deep-sea and hydrothermal vent habitats represent ancient ecosystems, and demonstrates a history of frequent dispersal between terrestrial and deep-sea habitats.

Present theories of tropical rain forest regeneration dynamics suggest that different tree species specialize on the microclimates of different sizes of canopy gap. A detailed analysis of the microclimates of closed forest and 10 canopy gaps of different sizes was carried out in lowland dipterocarp rain forest, Sabah, Malaysian Borneo. It reveals that gaps exhibit considerable spatial and temporal variation in microclimate. As a consequence the relationship between microclimate and gap sizes is not simple. Gaps of the same size do not necessarily have the same microclimate and may favour the growth of different seedling species. Chance location and timing of gap creation play an important role in regeneration dynamics.

Study of forest dynamics commonly requires measurement of canopy gap size. Hemispherical photographs can be analysed to provide various measures whereby gaps can be ranked in order of size. For ten artificial gaps in a Bornean tropical rain forest these measures were better correlated with gap microclimate than gap area measured physically on the ground. All these measures are however relative. For detailed (e.g. ecophysiological) studies the greater detail provided by absolute measures of photosynthetically active radiation (PAR) are required. Long term PAR values can be computed from hemiphots so long as measurements in the open nearby are available. Correction for cloudy weather is essential. Computed and measured PAR are compared for the test gaps. Both have inherent limits which means that below c. 15% canopy openness, differences in PAR between gaps cannot be assessed accurately.

Although sacred groves are important for conservation in India, the landscape that surrounds them has a vital influence on biodiversity within them. Research has focused on tree diversity inside these forest patches. In a coffee-growing region of the Western Ghats, however, landscape outside sacred groves is also tree covered because planters have retained native trees to provide shade for coffee plants. We examined the diversity of trees, birds, and macrofungi at 58 sites-10 forest-reserve sites, 25 sacred groves, and 23 coffee plantations-in Kodagu district. We measured landscape composition and configuration around each site with a geographic information system. To identify factors associated with diversity we constructed multivariate models by using a decision-tree technique. The conventional measures of landscape fragmentation such as patch size did not influence species richness. Distance of sacred groves from the forest reserve had a weak influence. The measures of landscape structure (e.g., tree cover in the surroundings) and stand structure (e.g., variability in canopy height) contributed to the variation in species richness explained by multivariate models. We suggest that biodiversity present within sacred groves has been influenced by native tree cover in the surrounding landscape. To conserve this biodiversity the integrity of the tree-covered landscape matrix will need to be conserved.Resumen: Aunque los bosques sagrados son importantes para la conservación en India, el paisaje que los rodea tiene una influencia vital sobre su biodiversidad. La investigación se ha centrado en la diversidad dé arboles dentro de estos parches de bosque. Sin embargo, en una región cafetalera de los Ghats Occidentales, el paisaje también es arbolado porque los dueños han retenidoárboles nativos para que proporcionen sombra a las plantas de café. Examinamos la diversidad deárboles, aves y macro hongos en 58 sitios, incluyendo 10 sitios en reservas forestales, 25 bosques sagrados y 23 plantaciones de café en el distrito Kodagu. Medimos la composición y configuración del paisaje alrededor de cada sitio con un sistema de información geográfica. Construimos modelos multivariados con la técnica deárbol de decisiones para identificar factores asociados con la diversidad. Las medidas convencionales de la fragmentación del paisaje, como tamaño del parche, no influyeron sobre la riqueza de especies. La distancia entre bosques sagrados y las reservas forestales tuvo una influencia débil. Las medidas de la estructura del paisaje (e. g., cobertura deárboles en los alrededores) y estructura del bosque (e. g., variabilidad en la altura del dosel) contribuyeron a la variación en la riqueza de especies explicada por los modelos multivariados. Sugerimos que la biodiversidad presente en los bosques sagrados ha sido influenciada por la cobertura deárboles nativos en el paisaje circundante. Para conservar esta biodiversidad, será necesario conservar la integridad de la matriz del paisaje arbolado.

Although it is widely believed that an important function of protected areas is to conserve species that are unable to survive elsewhere, there are very few empirical studies in which a comparison is made between biodiversity of protected areas and that of the cultivated landscape surrounding them. We examined the diversity of trees, birds, and macrofungi at 58 sites in three land-use types in a tree-covered landscape in Kodagu district in the Western Ghats of India. Ten forest reserve sites in the formal protected area, and 25 sacred groves and 23 coffee plantations in the neighboring cultivated landscape were sampled. A total of 215 tree, 86 bird, and 163 macrofungus species were recorded. The forest reserve had a large number of trees that were restricted in their distribution, and the sacred groves had a large number of macrofungi. We observed that deciduous trees and non-forest-dwelling birds increased, and evergreen trees and forest-dwelling birds decreased with increasing intensity of land management. We found that trees having non-timber uses and macrofungi useful to the local people, as well as those with medicinal properties, were abundant in sacred groves. We found no significant differences in the distribution of endemic and threatened birds across the three land-use types. Although endemic trees were more abundant in the forest reserve than in sacred groves, threatened trees were more abundant in sacred groves than in the forest reserve. We attribute the high diversity in sacred groves to the native tree cover in shade coffee plantations. We conclude that informal protected areas are as important as formal ones for biodiversity conservation in Kodagu. We recommend that a conservation strategy that recognizes informal protection traditions is essential for successful biodiversity conservation in regions where formal reserves are surrounded by a matrix of cultivated land.

Summary1. The high spatial and temporal variability of forest understorey light environments requires lengthy and/or extensive sampling in order to characterize it by direct measurement. As this is often impractical, a number of surrogate measures have been developed that estimate light availability from assessments of forest canopy structure. 2. The subjective crown illumination index developed by Clark & Clark (1992) was compared with Garrison's (1949) moosehorn and two new methods: (i) the crown illumination ellipses method, which compares the size of canopy gaps with a series of standard area ellipses printed on a transparent screen; and (ii) the canopy-scope that, like the moosehorn, uses an array of 25 dots printed on a transparent screen to assess canopy openness, but is more robust and portable, measuring the largest canopy gap visible from the point of measurement rather than canopy openness overhead. 3. The new measures were more highly correlated with canopy openness in the range 0±30%, measured from hemispherical photographs, than the crown illumination index, and showed lower levels of between-observer variability. 4. The canopy-scope has the potential to be widely used for the simple and rapid assessment of forest understorey light environments. It has the advantage of giving ratio scale measurements that can be used in parametric statistics. The crown illumination ellipses can be used to score the illumination of crowns that are above head height.

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Summary 1.Despite their functional importance, little is known about how and where fungi can be conserved. It is important that we understand the consequences of habitat degradation and fragmentation for fungal assemblages if we are to devise successful conservation strategies. 2. We investigated the effects of fragmentation and disturbance on the diversity and landscape distribution of fungi in tropical rain forests in the Kodagu district of the Western Ghats of India. We recorded macrofungi on three occasions over a wet season, in 0·125-ha plots in 10 forest reserve sites, 25 sacred groves and 23 coffee plantations. 3. Despite a long history of isolation from continuous forest, sacred groves had the highest sporocarp abundance and the greatest morphotype richness per sample area, while coffee plantations had the lowest. However, coffee plantation samples were more diverse for a given number of sporocarps than a sample of a similar size from other forest types. 4. Ordination by non-metric multidimensional scaling suggested that sacred groves had a macrofungal assemblage that was distinct from other forest types. This compositional difference was primarily because of the presence of a group of dead wood and litter decomposing fungi. Coffee plantations and forest reserve sites had very variable but overlapping compositions. 5. Neither sacred grove size nor distances between a grove and continuous forest accounted for a significant proportion of the total variation in their macrofungal richness. 6. There was no significant correlation between dissimilarity in macrofungal assemblage composition and geographical distance between sample sites. However, we found strong congruence between patterns of dissimilarity in macrofungi and trees between sites. 7. Synthesis and applications . These results imply that macrofungal distribution patterns at a landscape scale are determined by habitat requirements rather than dispersal or local population dynamics. This means that habitat degradation is a more serious threat to fungal diversity than fragmentation. Sacred groves, although small, are important for fungus conservation because they provide unique types of habitat.