The distribution of coastal fish eDNA sequences in the Anthropocene

Aim

Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio-economic factors.

Location

Tropical, temperate and polar coastal areas.

Time period

Present day.

Major taxa studied

Marine fishes.

Methods

We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio-economic factors on α- and β-diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic α- and β-diversity measured from our barcodes, and phylogenetic but also functional diversity.

Results

We show that fish eDNA MOTU and sequence α- and β-diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity.

Main conclusions

Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions.     

Cryptic diversity in Indo-Australian rainbowfishes revealed by DNA barcoding: implications for conservation in a biodiversity hotspot candidate

The rainbowfishes of the family Melanotaeniidae represent one of the largest radiations of freshwater fishes from the Indo-Australian archipelago. A total of 75 nominal species have been described, among which several have become very popular among tropical fish hobbyists because of their tendency to form large schools of colourful individuals. Facing habitat loss and competition or predation by introduced species, this group has become a priority in the conservation of ornamental fishes in Indonesia. In this context, several expeditions have been conducted between 2007 and 2010 in Indonesian Papua with the aim to initiate a large-scale survey of the genetic resources in this group. We assessed the diversity of the Papua rainbowfishes with DNA barcoding. We sequenced the mitochondrial COI gene for 350 specimens belonging to 53 nominal species throughout the Indo-Australian archipelago. Unexpected levels of cryptic diversity and endemism were detected since additional cryptic lineages were detected in several watersheds from the Vogelkop and the Lengguru massif. DNA barcoding supports the presence of nearly 30 evolutionary lineages among the 15 nominal species sampled in the Vogelkop and all these lineages are endemic to a single lake or watershed. This result highlights that the diversity of the family has been largely underestimated and urges for the identification of conservation priorities in Papua.     

Studies on the availability of Azolla N and urea N for rice growth using 15N

Field experiments (20 m² plots) were conducted to compare Azolla and urea as N sources for rice (Oryza sativa L.) in both the wet and dry seasons. Parallel microplot (1 m²) experiments were conducted using ¹⁵N. A total of approximately 60 kg N ha^-1 was applied as urea, Azolla, or urea plus Azolla. Urea or Azolla applied with equal applications of 30 kg N ha^-1 at transplanting (T) and at maximum tillering (MT) were equally effective for increasing rice grain yields in both seasons. Urea at 30 kg N ha^-1 at T and Azolla 30 kg N ha^-1 at MT was also equally effective. Urea applied by the locally recommended best split (40 kg at T and 20 kg at MT) gave a higher yield in the wet season, but an equal yield in the dry season. The average yield increase was 23% in the wet season, and 95% in the dry season. The proportion of the N taken up by the rice plants which was derived from urea (%NdfU) or Azolla (%NdfAz) was essentially identical for the treatments receiving the same N split. Recovery of ¹⁵N in the grain plus straw was also very similar. Positive yield responses to residual N were observed in the succeeding rice crop following both the wet and dry seasons, but the increases were not always statistically significant. Recovery of residual ¹⁵N ranged from 5.5 to 8.9% for both crops in succeeding seasons. Residual recovery from the urea applications was significantly higher than from Azolla in the crop succeeding the dry season crop. Azolla was equally effective as urea as an N source for rice production on a per kg N basis.     

Development of twelve novel polymorphic microsatellite DNA markers for the Boeseman’s rainbowfish (Melanotaenia boesemani) and tests for their cross-utility in 21 rainbowfish species from West Papua (Indonesia)

We developed 12 microsatellite markers for the endangered Boeseman’s rainbowfish (Melanotaenia boesemani). Twenty-eight individuals from the type locality at Ayamaru Lake were examined, and all loci were polymorphic with a number of alleles per locus varying from 3 to 18. Average observed and expected heterozygosities were 0.681 and 0.678, respectively. Cross-species amplification was successfully obtained for 21 Melanotaenia species, with a number of alleles per locus ranging between 1 and 20. Average observed and expected heterozygosities varied between 0.105 and 0.708 and 0.118–0.755, respectively. Only 21 inbreeding coefficient (Fis) values presented a significant homozygote excess among the 264 locus-by-locus calculated values. Tests for genotyping errors revealed that four of these 21 significant Fis values could be explained by the presence of null alleles. These new microsatellite markers appear highly reliable for further conservation purposes or population genetic studies of the many rainbowfish endangered species.     

Growing cholesterol-dependent NS0 myeloma cell line in the wave bioreactor system: overcoming cholesterol-polymer interaction by using pretreated polymer or inert fluorinated ethylene propylene

Difficulty in growing cholesterol-dependent NS0 cells in the Wave bioreactor using the original low-density polypropylene (LDPE) bags has been encountered. It has been shown that in these bags chemically defined cholesterol is depleted from solution and therefore unavailable for the cells. Our data suggest that the cause of the depletion is not chemical but is due to the physical structure of the polymer. It is proposed that polymer structures with inkbottle pores retain cholesterol, whereas structures with V-shaped pores adsorb cholesterol reversibly. Ultra-low-density polyethylene (ULDPE) bags can support cell growth but need to be pretreated with excess cholesterol. Another material, fluorinated ethylene propylene (FEP) does not need to be pretreated and is found to be superior (negligible cholesterol adsorption) as a result of its inert characteristics.