Edit

Template Coding Drupal Nested-query approach to mining field_collection data and relationship 

<?php

function get_species_country($id_country) {
    $inner = new EntityFieldQuery();
    $inner_r = $inner->entityCondition('entity_type', 'field_collection_item')
                     ->fieldCondition('field_species_country', 'target_id', $id_country, '=')
                     ->execute();
    if(!empty($inner_r['field_collection_item'])) {
        $keys = array_keys($inner_r['field_collection_item']);
        $query = new EntityFieldQuery();
        $species_r = $query->entityCondition('entity_type', 'node')
                      ->entityCondition('bundle', self::$bundle)
                      ->fieldCondition('field_species_countries', 'value', $keys)
                      ->execute();
        if(!empty($species_r['node'])) {
            $ret = node_load_multiple(array_keys($species_r['node']));
        }
    }
    return $ret;
}

?>